Starting phenix.real_space_refine on Tue Nov 18 06:15:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6fq6_4298/11_2025/6fq6_4298.cif Found real_map, /net/cci-nas-00/data/ceres_data/6fq6_4298/11_2025/6fq6_4298.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 { model { file = "/net/cci-nas-00/data/ceres_data/6fq6_4298/11_2025/6fq6_4298.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6fq6_4298/11_2025/6fq6_4298.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6fq6_4298/11_2025/6fq6_4298.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6fq6_4298/11_2025/6fq6_4298.map" } 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= 0.003 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 294 5.49 5 S 12 5.16 5 C 6620 2.51 5 N 2249 2.21 5 O 2812 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11987 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "B" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 668 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 832 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 699 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "E" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "F" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 832 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 690 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "I" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Time building chain proxies: 2.75, per 1000 atoms: 0.23 Number of scatterers: 11987 At special positions: 0 Unit cell: (77, 121.8, 112, 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 12 16.00 P 294 15.00 O 2812 8.00 N 2249 7.00 C 6620 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: 0.80 Conformation dependent library (CDL) restraints added in 344.8 milliseconds 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1412 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 9 sheets defined 73.5% alpha, 2.4% beta 147 base pairs and 260 stacking pairs defined. Time for finding SS restraints: 1.78 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.744A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 28 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 47 through 76 removed outlier: 3.940A pdb=" N TYR B 51 " --> pdb=" O SER B 47 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLU B 52 " --> pdb=" O GLY B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.802A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 36 removed outlier: 3.596A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.492A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.684A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.754A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 120 removed outlier: 3.691A pdb=" N ALA D 104 " --> pdb=" O PRO D 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.685A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 28 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 47 through 76 removed outlier: 4.048A pdb=" N TYR F 51 " --> pdb=" O SER F 47 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLU F 52 " --> pdb=" O GLY F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.708A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.426A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.872A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.511A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 121 removed outlier: 3.567A pdb=" N ALA H 104 " --> pdb=" O PRO H 100 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.515A 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 removed outlier: 3.551A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.727A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.915A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.823A 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 removed outlier: 3.634A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.657A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (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 78 395 hydrogen bonds defined for protein. 1167 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 376 hydrogen bonds 744 hydrogen bond angles 0 basepair planarities 147 basepair parallelities 260 stacking parallelities Total time for adding SS restraints: 2.36 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1413 1.32 - 1.44: 4792 1.44 - 1.56: 5985 1.56 - 1.68: 588 1.68 - 1.80: 22 Bond restraints: 12800 Sorted by residual: bond pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 1.422 1.496 -0.074 3.00e-02 1.11e+03 6.07e+00 bond pdb=" C3' DC I 52 " pdb=" O3' DC I 52 " ideal model delta sigma weight residual 1.422 1.492 -0.070 3.00e-02 1.11e+03 5.50e+00 bond pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " ideal model delta sigma weight residual 1.422 1.491 -0.069 3.00e-02 1.11e+03 5.32e+00 bond pdb=" C3' DG J 52 " pdb=" O3' DG J 52 " ideal model delta sigma weight residual 1.422 1.488 -0.066 3.00e-02 1.11e+03 4.78e+00 bond pdb=" C2 DC I 61 " pdb=" O2 DC I 61 " ideal model delta sigma weight residual 1.237 1.196 0.041 2.00e-02 2.50e+03 4.22e+00 ... (remaining 12795 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 17353 2.13 - 4.26: 1079 4.26 - 6.40: 105 6.40 - 8.53: 14 8.53 - 10.66: 4 Bond angle restraints: 18555 Sorted by residual: angle pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DG I 21 " ideal model delta sigma weight residual 120.20 127.48 -7.28 1.50e+00 4.44e-01 2.35e+01 angle pdb=" O4' DC I -26 " pdb=" C1' DC I -26 " pdb=" N1 DC I -26 " ideal model delta sigma weight residual 108.40 101.87 6.53 1.50e+00 4.44e-01 1.90e+01 angle pdb=" O4' DG I 4 " pdb=" C1' DG I 4 " pdb=" N9 DG I 4 " ideal model delta sigma weight residual 108.40 114.63 -6.23 1.50e+00 4.44e-01 1.72e+01 angle pdb=" O4' DC I -28 " pdb=" C1' DC I -28 " pdb=" N1 DC I -28 " ideal model delta sigma weight residual 108.40 102.36 6.04 1.50e+00 4.44e-01 1.62e+01 angle pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " pdb=" P DC I -58 " ideal model delta sigma weight residual 120.20 126.24 -6.04 1.50e+00 4.44e-01 1.62e+01 ... (remaining 18550 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.22: 5496 32.22 - 64.45: 1400 64.45 - 96.67: 36 96.67 - 128.90: 4 128.90 - 161.12: 2 Dihedral angle restraints: 6938 sinusoidal: 4752 harmonic: 2186 Sorted by residual: dihedral pdb=" C4' DT I -59 " pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " pdb=" P DC I -58 " ideal model delta sinusoidal sigma weight residual 220.00 58.88 161.12 1 3.50e+01 8.16e-04 1.53e+01 dihedral pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DG I 21 " ideal model delta sinusoidal sigma weight residual 220.00 64.07 155.93 1 3.50e+01 8.16e-04 1.50e+01 dihedral pdb=" C4' DC I 52 " pdb=" C3' DC I 52 " pdb=" O3' DC I 52 " pdb=" P DC I 53 " ideal model delta sinusoidal sigma weight residual 220.00 103.74 116.26 1 3.50e+01 8.16e-04 1.13e+01 ... (remaining 6935 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1771 0.088 - 0.176: 322 0.176 - 0.263: 24 0.263 - 0.351: 2 0.351 - 0.439: 1 Chirality restraints: 2120 Sorted by residual: chirality pdb=" C1' DG I 4 " pdb=" O4' DG I 4 " pdb=" C2' DG I 4 " pdb=" N9 DG I 4 " both_signs ideal model delta sigma weight residual False 2.42 1.98 0.44 2.00e-01 2.50e+01 4.81e+00 chirality pdb=" C1' DG I 20 " pdb=" O4' DG I 20 " pdb=" C2' DG I 20 " pdb=" N9 DG I 20 " both_signs ideal model delta sigma weight residual False 2.42 2.11 0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" C1' DG I -21 " pdb=" O4' DG I -21 " pdb=" C2' DG I -21 " pdb=" N9 DG I -21 " both_signs ideal model delta sigma weight residual False 2.42 2.15 0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 2117 not shown) Planarity restraints: 1326 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC I 61 " 0.001 2.00e-02 2.50e+03 3.07e-02 2.12e+01 pdb=" N1 DC I 61 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DC I 61 " -0.071 2.00e-02 2.50e+03 pdb=" O2 DC I 61 " 0.046 2.00e-02 2.50e+03 pdb=" N3 DC I 61 " 0.008 2.00e-02 2.50e+03 pdb=" C4 DC I 61 " -0.025 2.00e-02 2.50e+03 pdb=" N4 DC I 61 " 0.018 2.00e-02 2.50e+03 pdb=" C5 DC I 61 " 0.008 2.00e-02 2.50e+03 pdb=" C6 DC I 61 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I -28 " 0.065 2.00e-02 2.50e+03 3.01e-02 2.03e+01 pdb=" N1 DC I -28 " -0.040 2.00e-02 2.50e+03 pdb=" C2 DC I -28 " -0.013 2.00e-02 2.50e+03 pdb=" O2 DC I -28 " -0.010 2.00e-02 2.50e+03 pdb=" N3 DC I -28 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DC I -28 " 0.005 2.00e-02 2.50e+03 pdb=" N4 DC I -28 " 0.033 2.00e-02 2.50e+03 pdb=" C5 DC I -28 " -0.009 2.00e-02 2.50e+03 pdb=" C6 DC I -28 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I -26 " 0.060 2.00e-02 2.50e+03 2.99e-02 2.01e+01 pdb=" N1 DC I -26 " -0.047 2.00e-02 2.50e+03 pdb=" C2 DC I -26 " -0.002 2.00e-02 2.50e+03 pdb=" O2 DC I -26 " -0.018 2.00e-02 2.50e+03 pdb=" N3 DC I -26 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DC I -26 " 0.007 2.00e-02 2.50e+03 pdb=" N4 DC I -26 " 0.032 2.00e-02 2.50e+03 pdb=" C5 DC I -26 " -0.029 2.00e-02 2.50e+03 pdb=" C6 DC I -26 " -0.004 2.00e-02 2.50e+03 ... (remaining 1323 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2243 2.79 - 3.32: 11197 3.32 - 3.84: 25040 3.84 - 4.37: 28236 4.37 - 4.90: 39457 Nonbonded interactions: 106173 Sorted by model distance: nonbonded pdb=" OG SER G 18 " pdb=" O PHE G 25 " model vdw 2.261 3.040 nonbonded pdb=" OG SER C 18 " pdb=" O PHE C 25 " model vdw 2.272 3.040 nonbonded pdb=" O VAL H 108 " pdb=" OG1 THR H 112 " model vdw 2.307 3.040 nonbonded pdb=" NZ LYS D 43 " pdb=" O PRO D 47 " model vdw 2.321 3.120 nonbonded pdb=" O VAL D 108 " pdb=" OG1 THR D 112 " model vdw 2.333 3.040 ... (remaining 106168 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' and resid 20 through 101) selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 33 through 121) 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: 0.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.880 Find NCS groups from input model: 0.130 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 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 : 0.009 0.074 12800 Z= 0.383 Angle : 1.104 10.662 18555 Z= 0.656 Chirality : 0.066 0.439 2120 Planarity : 0.008 0.040 1326 Dihedral : 26.701 161.124 5526 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.32 % Allowed : 1.44 % Favored : 98.24 % 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: -0.84 (0.27), residues: 736 helix: -0.06 (0.20), residues: 522 sheet: None (None), residues: 0 loop : -1.57 (0.35), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 11 TYR 0.032 0.004 TYR A 54 PHE 0.021 0.004 PHE E 78 HIS 0.011 0.003 HIS C 82 Details of bonding type rmsd covalent geometry : bond 0.00852 (12800) covalent geometry : angle 1.10432 (18555) hydrogen bonds : bond 0.13524 ( 771) hydrogen bonds : angle 5.78257 ( 1911) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 308 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.6281 (mt) cc_final: 0.5846 (mt) REVERT: A 93 GLN cc_start: 0.8110 (tt0) cc_final: 0.7802 (tt0) REVERT: A 100 LEU cc_start: 0.9279 (mt) cc_final: 0.9033 (pp) REVERT: A 120 MET cc_start: 0.7083 (mtp) cc_final: 0.6082 (mtp) REVERT: A 124 ILE cc_start: 0.9470 (mt) cc_final: 0.8922 (mp) REVERT: A 129 ARG cc_start: 0.9134 (mtp180) cc_final: 0.8643 (mmm160) REVERT: B 59 LYS cc_start: 0.9096 (ttpt) cc_final: 0.8877 (tppt) REVERT: B 70 VAL cc_start: 0.9337 (t) cc_final: 0.9069 (t) REVERT: B 88 TYR cc_start: 0.8315 (m-10) cc_final: 0.7669 (m-80) REVERT: B 96 THR cc_start: 0.8707 (m) cc_final: 0.8450 (p) REVERT: C 61 GLU cc_start: 0.9202 (tp30) cc_final: 0.8888 (tm-30) REVERT: C 84 GLN cc_start: 0.8066 (tp40) cc_final: 0.7166 (tp40) REVERT: C 94 ASN cc_start: 0.8432 (t0) cc_final: 0.8114 (t0) REVERT: C 113 SER cc_start: 0.8820 (m) cc_final: 0.8586 (p) REVERT: D 34 TYR cc_start: 0.8699 (m-80) cc_final: 0.8438 (m-10) REVERT: D 41 VAL cc_start: 0.9538 (t) cc_final: 0.9322 (t) REVERT: D 51 ILE cc_start: 0.8376 (pt) cc_final: 0.8029 (tt) REVERT: D 73 GLU cc_start: 0.9177 (mm-30) cc_final: 0.8398 (tt0) REVERT: E 82 LEU cc_start: 0.5668 (mt) cc_final: 0.5356 (mt) REVERT: E 92 LEU cc_start: 0.9246 (mt) cc_final: 0.8991 (mt) REVERT: E 93 GLN cc_start: 0.8743 (tt0) cc_final: 0.7598 (tp-100) REVERT: E 106 ASP cc_start: 0.8654 (m-30) cc_final: 0.8346 (m-30) REVERT: E 120 MET cc_start: 0.7320 (mtp) cc_final: 0.6917 (mtt) REVERT: F 25 ASN cc_start: 0.5810 (m-40) cc_final: 0.5325 (m-40) REVERT: F 44 LYS cc_start: 0.7914 (tttt) cc_final: 0.7450 (tmmt) REVERT: F 60 VAL cc_start: 0.9127 (t) cc_final: 0.8880 (m) REVERT: F 70 VAL cc_start: 0.9311 (t) cc_final: 0.9065 (t) REVERT: F 88 TYR cc_start: 0.8243 (m-10) cc_final: 0.7772 (m-10) REVERT: G 35 ARG cc_start: 0.8699 (mtm180) cc_final: 0.8219 (mtp180) REVERT: G 64 GLU cc_start: 0.9426 (tt0) cc_final: 0.9135 (tp30) REVERT: G 94 ASN cc_start: 0.8753 (t0) cc_final: 0.8495 (t0) REVERT: H 34 TYR cc_start: 0.8028 (m-80) cc_final: 0.7799 (m-10) REVERT: H 37 TYR cc_start: 0.7736 (m-80) cc_final: 0.7450 (m-80) REVERT: H 73 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8259 (tt0) REVERT: H 103 LEU cc_start: 0.9257 (mt) cc_final: 0.8928 (mt) REVERT: H 106 HIS cc_start: 0.8454 (m-70) cc_final: 0.8092 (m90) outliers start: 2 outliers final: 2 residues processed: 310 average time/residue: 0.1481 time to fit residues: 60.7976 Evaluate side-chains 168 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 166 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain H residue 113 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN F 25 ASN F 27 GLN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN H 46 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.055968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.048423 restraints weight = 107813.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.049697 restraints weight = 65691.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.050599 restraints weight = 44583.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.051219 restraints weight = 32572.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.051693 restraints weight = 25461.571| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 12800 Z= 0.263 Angle : 0.743 10.382 18555 Z= 0.436 Chirality : 0.041 0.160 2120 Planarity : 0.006 0.042 1326 Dihedral : 31.686 174.426 4052 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 23.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.35 % Allowed : 19.17 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.29), residues: 736 helix: 0.93 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -1.45 (0.37), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 23 TYR 0.019 0.002 TYR G 57 PHE 0.018 0.002 PHE D 62 HIS 0.005 0.002 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00571 (12800) covalent geometry : angle 0.74324 (18555) hydrogen bonds : bond 0.07928 ( 771) hydrogen bonds : angle 4.28142 ( 1911) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 192 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.7239 (mtp) cc_final: 0.6917 (mtp) REVERT: B 59 LYS cc_start: 0.9541 (ttpt) cc_final: 0.9125 (tptp) REVERT: B 60 VAL cc_start: 0.9260 (p) cc_final: 0.8087 (m) REVERT: B 63 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8022 (pt0) REVERT: B 88 TYR cc_start: 0.8628 (m-10) cc_final: 0.8048 (m-80) REVERT: C 61 GLU cc_start: 0.9208 (tp30) cc_final: 0.8898 (tm-30) REVERT: D 34 TYR cc_start: 0.8264 (m-80) cc_final: 0.7983 (m-80) REVERT: D 73 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8702 (tp30) REVERT: D 106 HIS cc_start: 0.8346 (m-70) cc_final: 0.7935 (m90) REVERT: E 93 GLN cc_start: 0.8344 (tt0) cc_final: 0.7220 (tp-100) REVERT: E 97 GLU cc_start: 0.7939 (mt-10) cc_final: 0.6530 (mt-10) REVERT: E 100 LEU cc_start: 0.9597 (mt) cc_final: 0.9384 (mm) REVERT: E 103 LEU cc_start: 0.9237 (pp) cc_final: 0.8940 (mt) REVERT: F 25 ASN cc_start: 0.6197 (m110) cc_final: 0.5781 (m-40) REVERT: F 44 LYS cc_start: 0.8047 (tttt) cc_final: 0.7582 (ttpt) REVERT: F 88 TYR cc_start: 0.8520 (m-10) cc_final: 0.8065 (m-10) REVERT: G 57 TYR cc_start: 0.8398 (t80) cc_final: 0.8037 (t80) REVERT: G 64 GLU cc_start: 0.9269 (tt0) cc_final: 0.8805 (tp30) REVERT: G 84 GLN cc_start: 0.8663 (tp40) cc_final: 0.8409 (tt0) REVERT: H 39 TYR cc_start: 0.8614 (OUTLIER) cc_final: 0.7962 (m-80) REVERT: H 73 GLU cc_start: 0.9151 (mm-30) cc_final: 0.8663 (tp30) outliers start: 21 outliers final: 13 residues processed: 200 average time/residue: 0.1138 time to fit residues: 32.3000 Evaluate side-chains 154 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 55 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 51 TYR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 39 TYR Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 87 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 73 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 7 optimal weight: 0.0020 chunk 21 optimal weight: 5.9990 overall best weight: 3.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.056829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.049185 restraints weight = 109911.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.050465 restraints weight = 67172.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.051336 restraints weight = 45599.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.051963 restraints weight = 33571.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.052395 restraints weight = 26225.528| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 12800 Z= 0.216 Angle : 0.705 13.056 18555 Z= 0.407 Chirality : 0.039 0.163 2120 Planarity : 0.005 0.044 1326 Dihedral : 31.412 169.530 4048 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 20.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.67 % Allowed : 21.57 % Favored : 74.76 % 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: 0.48 (0.29), residues: 736 helix: 1.01 (0.21), residues: 539 sheet: None (None), residues: 0 loop : -1.53 (0.38), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 116 TYR 0.018 0.002 TYR H 37 PHE 0.023 0.002 PHE D 62 HIS 0.004 0.002 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00471 (12800) covalent geometry : angle 0.70473 (18555) hydrogen bonds : bond 0.06431 ( 771) hydrogen bonds : angle 4.06417 ( 1911) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 169 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8662 (mmt) cc_final: 0.8449 (mmm) REVERT: A 100 LEU cc_start: 0.9275 (mm) cc_final: 0.9029 (pp) REVERT: A 103 LEU cc_start: 0.9380 (mt) cc_final: 0.9115 (mt) REVERT: A 104 PHE cc_start: 0.8995 (m-80) cc_final: 0.8769 (m-80) REVERT: B 25 ASN cc_start: 0.5391 (m110) cc_final: 0.5029 (m110) REVERT: B 88 TYR cc_start: 0.8620 (m-10) cc_final: 0.7993 (m-80) REVERT: C 61 GLU cc_start: 0.9199 (tp30) cc_final: 0.8947 (tm-30) REVERT: D 34 TYR cc_start: 0.8100 (m-80) cc_final: 0.7861 (m-80) REVERT: D 73 GLU cc_start: 0.9012 (mm-30) cc_final: 0.8671 (tp30) REVERT: D 106 HIS cc_start: 0.8339 (m-70) cc_final: 0.7875 (m90) REVERT: E 93 GLN cc_start: 0.8267 (tt0) cc_final: 0.7135 (tp40) REVERT: E 97 GLU cc_start: 0.7987 (mt-10) cc_final: 0.6639 (mt-10) REVERT: E 103 LEU cc_start: 0.9267 (pp) cc_final: 0.9028 (mt) REVERT: E 106 ASP cc_start: 0.9063 (m-30) cc_final: 0.8813 (t70) REVERT: F 25 ASN cc_start: 0.5612 (m110) cc_final: 0.5318 (m-40) REVERT: F 44 LYS cc_start: 0.8061 (tttt) cc_final: 0.7482 (tttm) REVERT: F 59 LYS cc_start: 0.9275 (tptp) cc_final: 0.9069 (tppt) REVERT: F 88 TYR cc_start: 0.8458 (m-10) cc_final: 0.8024 (m-10) REVERT: G 64 GLU cc_start: 0.9219 (tt0) cc_final: 0.8722 (tp30) REVERT: G 84 GLN cc_start: 0.8652 (tp40) cc_final: 0.8434 (tt0) REVERT: G 94 ASN cc_start: 0.8330 (OUTLIER) cc_final: 0.8074 (m-40) REVERT: H 73 GLU cc_start: 0.9144 (mm-30) cc_final: 0.8444 (tp30) REVERT: H 77 LEU cc_start: 0.9004 (mm) cc_final: 0.8574 (mm) REVERT: H 106 HIS cc_start: 0.8629 (t-90) cc_final: 0.8276 (t-90) outliers start: 23 outliers final: 15 residues processed: 180 average time/residue: 0.1072 time to fit residues: 27.6358 Evaluate side-chains 151 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 64 ASN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 55 GLN Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 87 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 60 optimal weight: 0.9990 chunk 40 optimal weight: 0.0980 chunk 12 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 8 optimal weight: 0.4980 chunk 71 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.057585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.049879 restraints weight = 110022.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.051143 restraints weight = 66965.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.052019 restraints weight = 45566.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.052631 restraints weight = 33618.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.053086 restraints weight = 26479.390| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12800 Z= 0.189 Angle : 0.683 11.030 18555 Z= 0.392 Chirality : 0.038 0.194 2120 Planarity : 0.005 0.045 1326 Dihedral : 31.285 166.787 4048 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 19.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.99 % Allowed : 21.25 % Favored : 74.76 % 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: 0.40 (0.29), residues: 736 helix: 1.04 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -1.76 (0.36), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 116 TYR 0.017 0.001 TYR D 37 PHE 0.024 0.002 PHE D 62 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00409 (12800) covalent geometry : angle 0.68265 (18555) hydrogen bonds : bond 0.05630 ( 771) hydrogen bonds : angle 3.92561 ( 1911) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8646 (mmt) cc_final: 0.8421 (mmm) REVERT: A 103 LEU cc_start: 0.9444 (mt) cc_final: 0.9188 (mt) REVERT: B 25 ASN cc_start: 0.5589 (m110) cc_final: 0.5371 (m110) REVERT: B 63 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8303 (mm-30) REVERT: B 88 TYR cc_start: 0.8590 (m-10) cc_final: 0.8062 (m-80) REVERT: C 61 GLU cc_start: 0.9169 (tp30) cc_final: 0.8778 (tm-30) REVERT: D 34 TYR cc_start: 0.8101 (m-80) cc_final: 0.7814 (m-80) REVERT: D 73 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8610 (tp30) REVERT: D 102 GLU cc_start: 0.9085 (tp30) cc_final: 0.8596 (tm-30) REVERT: D 106 HIS cc_start: 0.8246 (m-70) cc_final: 0.7665 (m170) REVERT: E 93 GLN cc_start: 0.8307 (tt0) cc_final: 0.7273 (tt0) REVERT: E 97 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7673 (mt-10) REVERT: F 25 ASN cc_start: 0.5568 (m110) cc_final: 0.5273 (m-40) REVERT: F 59 LYS cc_start: 0.9336 (tptp) cc_final: 0.8837 (tppt) REVERT: F 88 TYR cc_start: 0.8436 (m-10) cc_final: 0.8004 (m-10) REVERT: F 100 PHE cc_start: 0.8276 (m-80) cc_final: 0.7961 (m-80) REVERT: G 64 GLU cc_start: 0.9194 (tt0) cc_final: 0.8651 (tp30) REVERT: G 84 GLN cc_start: 0.8609 (tp40) cc_final: 0.8385 (tt0) REVERT: G 90 ASP cc_start: 0.7845 (t70) cc_final: 0.7459 (t0) REVERT: G 94 ASN cc_start: 0.8387 (t0) cc_final: 0.8031 (m110) REVERT: H 73 GLU cc_start: 0.9130 (mm-30) cc_final: 0.8559 (tp30) REVERT: H 106 HIS cc_start: 0.8551 (t-90) cc_final: 0.8125 (t-90) outliers start: 25 outliers final: 18 residues processed: 173 average time/residue: 0.1056 time to fit residues: 26.7011 Evaluate side-chains 152 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 55 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 87 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 84 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 17 optimal weight: 30.0000 chunk 26 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 30.0000 chunk 77 optimal weight: 10.0000 chunk 60 optimal weight: 0.9990 chunk 51 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 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 = 0.3632 r_free = 0.3632 target = 0.056745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.049132 restraints weight = 112705.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.050345 restraints weight = 69067.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.051190 restraints weight = 47383.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.051770 restraints weight = 35222.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.052216 restraints weight = 28088.752| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.4884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12800 Z= 0.208 Angle : 0.691 14.286 18555 Z= 0.397 Chirality : 0.038 0.193 2120 Planarity : 0.005 0.048 1326 Dihedral : 31.357 165.520 4048 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 21.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 4.47 % Allowed : 22.20 % Favored : 73.32 % 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: 0.29 (0.29), residues: 736 helix: 0.98 (0.22), residues: 529 sheet: None (None), residues: 0 loop : -1.83 (0.36), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 67 TYR 0.020 0.002 TYR D 37 PHE 0.022 0.002 PHE D 62 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00450 (12800) covalent geometry : angle 0.69122 (18555) hydrogen bonds : bond 0.06272 ( 771) hydrogen bonds : angle 3.94007 ( 1911) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8359 (mm-30) cc_final: 0.7906 (mt-10) REVERT: A 103 LEU cc_start: 0.9459 (mt) cc_final: 0.9192 (mt) REVERT: B 25 ASN cc_start: 0.5682 (m110) cc_final: 0.5476 (m110) REVERT: B 88 TYR cc_start: 0.8582 (m-10) cc_final: 0.8025 (m-80) REVERT: C 61 GLU cc_start: 0.9090 (tp30) cc_final: 0.8717 (tm-30) REVERT: D 59 MET cc_start: 0.8821 (mmm) cc_final: 0.8544 (mmm) REVERT: D 73 GLU cc_start: 0.8967 (mm-30) cc_final: 0.8563 (tp30) REVERT: D 102 GLU cc_start: 0.9065 (tp30) cc_final: 0.8437 (tm-30) REVERT: D 106 HIS cc_start: 0.8047 (m-70) cc_final: 0.7355 (m90) REVERT: E 93 GLN cc_start: 0.8288 (tt0) cc_final: 0.7291 (tt0) REVERT: E 97 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7665 (mt-10) REVERT: F 25 ASN cc_start: 0.5638 (m110) cc_final: 0.5316 (m-40) REVERT: F 63 GLU cc_start: 0.8359 (mm-30) cc_final: 0.8071 (tm-30) REVERT: F 88 TYR cc_start: 0.8451 (m-10) cc_final: 0.7980 (m-10) REVERT: F 100 PHE cc_start: 0.8191 (m-80) cc_final: 0.7844 (m-80) REVERT: H 39 TYR cc_start: 0.8654 (OUTLIER) cc_final: 0.7963 (m-80) REVERT: H 51 ILE cc_start: 0.8745 (tt) cc_final: 0.8270 (mt) REVERT: H 73 GLU cc_start: 0.9076 (mm-30) cc_final: 0.8528 (tp30) outliers start: 28 outliers final: 18 residues processed: 163 average time/residue: 0.1036 time to fit residues: 24.9617 Evaluate side-chains 146 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 55 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 39 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 97 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 93 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 60 optimal weight: 0.8980 chunk 17 optimal weight: 30.0000 chunk 73 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.055807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.048297 restraints weight = 114233.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.049532 restraints weight = 70068.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.050403 restraints weight = 47966.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.051021 restraints weight = 35451.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.051474 restraints weight = 27884.966| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.5320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 12800 Z= 0.225 Angle : 0.707 11.696 18555 Z= 0.406 Chirality : 0.039 0.176 2120 Planarity : 0.005 0.050 1326 Dihedral : 31.525 165.762 4048 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 22.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.63 % Allowed : 23.32 % Favored : 72.04 % 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: -0.04 (0.29), residues: 736 helix: 0.66 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -1.76 (0.37), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 32 TYR 0.022 0.002 TYR D 37 PHE 0.020 0.002 PHE D 62 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00487 (12800) covalent geometry : angle 0.70667 (18555) hydrogen bonds : bond 0.06801 ( 771) hydrogen bonds : angle 4.05154 ( 1911) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 LEU cc_start: 0.9527 (mt) cc_final: 0.9245 (mt) REVERT: B 25 ASN cc_start: 0.5587 (m110) cc_final: 0.5297 (m110) REVERT: B 88 TYR cc_start: 0.8593 (m-10) cc_final: 0.8118 (m-80) REVERT: C 61 GLU cc_start: 0.9170 (tp30) cc_final: 0.8858 (tm-30) REVERT: D 37 TYR cc_start: 0.7663 (m-80) cc_final: 0.7263 (m-80) REVERT: D 73 GLU cc_start: 0.9121 (mm-30) cc_final: 0.8750 (tp30) REVERT: D 102 GLU cc_start: 0.9123 (tp30) cc_final: 0.8426 (tm-30) REVERT: D 106 HIS cc_start: 0.8208 (m-70) cc_final: 0.7529 (m90) REVERT: E 93 GLN cc_start: 0.8333 (tt0) cc_final: 0.7378 (tt0) REVERT: F 25 ASN cc_start: 0.5555 (m110) cc_final: 0.5196 (m-40) REVERT: F 88 TYR cc_start: 0.8544 (m-10) cc_final: 0.8096 (m-10) REVERT: F 100 PHE cc_start: 0.8170 (m-80) cc_final: 0.7747 (m-80) REVERT: H 73 GLU cc_start: 0.9145 (mm-30) cc_final: 0.8574 (tp30) REVERT: H 106 HIS cc_start: 0.8607 (t-90) cc_final: 0.8312 (t-90) outliers start: 29 outliers final: 23 residues processed: 156 average time/residue: 0.0968 time to fit residues: 22.7310 Evaluate side-chains 151 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 55 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 87 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 39 optimal weight: 6.9990 chunk 47 optimal weight: 8.9990 chunk 55 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 14 optimal weight: 0.6980 chunk 79 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.055307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.048306 restraints weight = 115276.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.049458 restraints weight = 72185.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.050243 restraints weight = 49943.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.050817 restraints weight = 37428.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.051222 restraints weight = 29653.803| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.5671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 12800 Z= 0.236 Angle : 0.730 12.695 18555 Z= 0.416 Chirality : 0.040 0.233 2120 Planarity : 0.005 0.043 1326 Dihedral : 31.662 166.554 4048 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 23.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.47 % Allowed : 25.08 % Favored : 70.45 % 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: -0.15 (0.29), residues: 736 helix: 0.58 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -1.82 (0.37), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 32 TYR 0.022 0.002 TYR D 37 PHE 0.020 0.002 PHE F 61 HIS 0.006 0.002 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00515 (12800) covalent geometry : angle 0.73022 (18555) hydrogen bonds : bond 0.07144 ( 771) hydrogen bonds : angle 4.16331 ( 1911) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ILE cc_start: 0.7900 (mt) cc_final: 0.7505 (mm) REVERT: A 103 LEU cc_start: 0.9434 (mt) cc_final: 0.9212 (mt) REVERT: B 25 ASN cc_start: 0.5742 (m110) cc_final: 0.5468 (m110) REVERT: B 88 TYR cc_start: 0.8593 (m-10) cc_final: 0.8075 (m-80) REVERT: C 61 GLU cc_start: 0.9027 (tp30) cc_final: 0.8781 (tm-30) REVERT: D 39 TYR cc_start: 0.8554 (OUTLIER) cc_final: 0.7582 (m-80) REVERT: D 73 GLU cc_start: 0.8992 (mm-30) cc_final: 0.8683 (tp30) REVERT: D 85 THR cc_start: 0.8282 (p) cc_final: 0.8044 (p) REVERT: D 102 GLU cc_start: 0.8985 (tp30) cc_final: 0.8218 (tm-30) REVERT: D 106 HIS cc_start: 0.7962 (m-70) cc_final: 0.7363 (m90) REVERT: D 117 LYS cc_start: 0.8919 (mttt) cc_final: 0.8706 (ptpp) REVERT: F 25 ASN cc_start: 0.5838 (m110) cc_final: 0.5483 (m-40) REVERT: F 88 TYR cc_start: 0.8494 (m-10) cc_final: 0.8022 (m-10) REVERT: F 100 PHE cc_start: 0.8003 (m-80) cc_final: 0.7555 (m-80) REVERT: G 113 SER cc_start: 0.8394 (m) cc_final: 0.8163 (p) REVERT: H 73 GLU cc_start: 0.9013 (mm-30) cc_final: 0.8391 (tp30) REVERT: H 106 HIS cc_start: 0.8366 (t-90) cc_final: 0.8022 (t-90) outliers start: 28 outliers final: 22 residues processed: 153 average time/residue: 0.0941 time to fit residues: 21.6492 Evaluate side-chains 151 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 39 TYR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 87 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 57 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 40 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 28 optimal weight: 0.7980 chunk 44 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 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 = 0.3696 r_free = 0.3696 target = 0.061759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.055209 restraints weight = 113388.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.056465 restraints weight = 67311.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.057427 restraints weight = 45009.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.058059 restraints weight = 31812.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.058557 restraints weight = 24104.221| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.5878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12800 Z= 0.186 Angle : 0.716 13.264 18555 Z= 0.401 Chirality : 0.040 0.498 2120 Planarity : 0.005 0.045 1326 Dihedral : 31.585 166.738 4048 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 19.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.19 % Allowed : 26.84 % Favored : 69.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.29), residues: 736 helix: 0.60 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -1.96 (0.37), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 67 TYR 0.016 0.002 TYR E 99 PHE 0.016 0.002 PHE F 61 HIS 0.003 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00404 (12800) covalent geometry : angle 0.71618 (18555) hydrogen bonds : bond 0.05435 ( 771) hydrogen bonds : angle 4.00441 ( 1911) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ILE cc_start: 0.7775 (mt) cc_final: 0.7391 (mm) REVERT: A 103 LEU cc_start: 0.9502 (mt) cc_final: 0.9258 (mt) REVERT: B 25 ASN cc_start: 0.5587 (m110) cc_final: 0.5352 (m110) REVERT: B 34 ILE cc_start: 0.9183 (mp) cc_final: 0.8902 (pt) REVERT: B 37 LEU cc_start: 0.8082 (mp) cc_final: 0.7716 (mp) REVERT: B 88 TYR cc_start: 0.8594 (m-10) cc_final: 0.8065 (m-10) REVERT: C 61 GLU cc_start: 0.9120 (tp30) cc_final: 0.8725 (tm-30) REVERT: D 73 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8512 (tp30) REVERT: D 85 THR cc_start: 0.8223 (p) cc_final: 0.7969 (p) REVERT: D 102 GLU cc_start: 0.8999 (tp30) cc_final: 0.8390 (tm-30) REVERT: D 106 HIS cc_start: 0.8107 (m-70) cc_final: 0.7667 (m90) REVERT: F 25 ASN cc_start: 0.5589 (m110) cc_final: 0.5240 (m-40) REVERT: F 88 TYR cc_start: 0.8394 (m-10) cc_final: 0.7952 (m-10) REVERT: F 100 PHE cc_start: 0.8081 (m-80) cc_final: 0.7581 (m-80) REVERT: G 56 GLU cc_start: 0.9206 (tt0) cc_final: 0.8805 (tt0) REVERT: H 56 MET cc_start: 0.7581 (tpt) cc_final: 0.7331 (tpt) REVERT: H 73 GLU cc_start: 0.9011 (mm-30) cc_final: 0.8394 (tp30) REVERT: H 106 HIS cc_start: 0.8354 (t-90) cc_final: 0.7982 (t-90) outliers start: 20 outliers final: 19 residues processed: 154 average time/residue: 0.0996 time to fit residues: 22.7871 Evaluate side-chains 143 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 87 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 89 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 chunk 81 optimal weight: 8.9990 chunk 52 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 28 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 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 = 0.3558 r_free = 0.3558 target = 0.053328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.046430 restraints weight = 117537.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.047515 restraints weight = 73329.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.048257 restraints weight = 50526.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.048816 restraints weight = 37783.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.049205 restraints weight = 29865.539| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.6296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 12800 Z= 0.310 Angle : 0.807 12.656 18555 Z= 0.458 Chirality : 0.044 0.454 2120 Planarity : 0.006 0.048 1326 Dihedral : 31.968 166.303 4048 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 31.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.19 % Allowed : 27.00 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.29), residues: 736 helix: 0.26 (0.21), residues: 531 sheet: None (None), residues: 0 loop : -1.94 (0.38), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 42 TYR 0.029 0.003 TYR D 37 PHE 0.023 0.002 PHE F 61 HIS 0.008 0.002 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00672 (12800) covalent geometry : angle 0.80747 (18555) hydrogen bonds : bond 0.09397 ( 771) hydrogen bonds : angle 4.46001 ( 1911) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.5682 (m110) cc_final: 0.5368 (m110) REVERT: B 34 ILE cc_start: 0.9135 (mp) cc_final: 0.8842 (pt) REVERT: B 37 LEU cc_start: 0.7977 (mp) cc_final: 0.7663 (mp) REVERT: B 88 TYR cc_start: 0.8581 (m-10) cc_final: 0.7971 (m-80) REVERT: C 61 GLU cc_start: 0.9077 (tp30) cc_final: 0.8831 (tm-30) REVERT: D 73 GLU cc_start: 0.9097 (mm-30) cc_final: 0.8808 (tp30) REVERT: D 102 GLU cc_start: 0.9074 (tp30) cc_final: 0.8676 (tm-30) REVERT: F 88 TYR cc_start: 0.8525 (m-10) cc_final: 0.8008 (m-10) REVERT: G 113 SER cc_start: 0.8342 (m) cc_final: 0.8141 (p) REVERT: H 73 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8280 (tp30) REVERT: H 106 HIS cc_start: 0.8492 (t-90) cc_final: 0.8126 (t-90) outliers start: 20 outliers final: 20 residues processed: 138 average time/residue: 0.1039 time to fit residues: 21.2633 Evaluate side-chains 137 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 87 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 87 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 chunk 61 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.053531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.046670 restraints weight = 116223.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.047754 restraints weight = 72660.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.048525 restraints weight = 50153.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.049082 restraints weight = 37312.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.049474 restraints weight = 29490.912| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.6588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 12800 Z= 0.278 Angle : 0.802 15.365 18555 Z= 0.452 Chirality : 0.045 0.610 2120 Planarity : 0.005 0.044 1326 Dihedral : 32.133 168.381 4048 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 28.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.67 % Allowed : 26.52 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.29), residues: 736 helix: 0.26 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -2.02 (0.38), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 42 TYR 0.027 0.003 TYR D 37 PHE 0.022 0.002 PHE F 61 HIS 0.008 0.002 HIS D 79 Details of bonding type rmsd covalent geometry : bond 0.00603 (12800) covalent geometry : angle 0.80211 (18555) hydrogen bonds : bond 0.08253 ( 771) hydrogen bonds : angle 4.40105 ( 1911) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ILE cc_start: 0.7740 (mt) cc_final: 0.7287 (mm) REVERT: B 25 ASN cc_start: 0.5976 (m110) cc_final: 0.5677 (m110) REVERT: B 88 TYR cc_start: 0.8541 (m-10) cc_final: 0.7987 (m-80) REVERT: C 61 GLU cc_start: 0.9002 (tp30) cc_final: 0.8794 (tm-30) REVERT: D 73 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8659 (tp30) REVERT: D 105 LYS cc_start: 0.9445 (mmmm) cc_final: 0.9072 (mmmm) REVERT: D 106 HIS cc_start: 0.7962 (m90) cc_final: 0.7519 (m90) REVERT: F 25 ASN cc_start: 0.6285 (m-40) cc_final: 0.5904 (m-40) REVERT: F 88 TYR cc_start: 0.8478 (m-10) cc_final: 0.7979 (m-10) REVERT: H 73 GLU cc_start: 0.8916 (mm-30) cc_final: 0.8427 (tp30) REVERT: H 106 HIS cc_start: 0.8530 (t-90) cc_final: 0.8308 (t-90) outliers start: 23 outliers final: 23 residues processed: 142 average time/residue: 0.0997 time to fit residues: 21.2395 Evaluate side-chains 144 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 97 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 13 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 21 optimal weight: 0.0270 chunk 81 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 overall best weight: 3.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 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 = 0.3602 r_free = 0.3602 target = 0.055419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.048428 restraints weight = 112405.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.049577 restraints weight = 70186.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.050366 restraints weight = 48142.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.050938 restraints weight = 35750.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.051361 restraints weight = 28228.786| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.6655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 12800 Z= 0.211 Angle : 0.761 16.575 18555 Z= 0.427 Chirality : 0.043 0.524 2120 Planarity : 0.005 0.043 1326 Dihedral : 32.022 168.934 4048 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 23.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.35 % Allowed : 27.80 % Favored : 68.85 % 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: -0.43 (0.30), residues: 736 helix: 0.38 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.94 (0.39), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 32 TYR 0.016 0.002 TYR H 37 PHE 0.023 0.002 PHE C 25 HIS 0.006 0.001 HIS D 79 Details of bonding type rmsd covalent geometry : bond 0.00458 (12800) covalent geometry : angle 0.76091 (18555) hydrogen bonds : bond 0.06569 ( 771) hydrogen bonds : angle 4.19612 ( 1911) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1657.25 seconds wall clock time: 29 minutes 35.26 seconds (1775.26 seconds total)