Starting phenix.real_space_refine on Fri Sep 11 21:14:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6fq6_4298/09_2026/6fq6_4298.cif Found real_map, /net/cci-nas-00/data/ceres_data/6fq6_4298/09_2026/6fq6_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_4298/09_2026/6fq6_4298.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6fq6_4298/09_2026/6fq6_4298.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6fq6_4298/09_2026/6fq6_4298.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6fq6_4298/09_2026/6fq6_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-2.2.1-6174/lib/python3.11/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: 0.94 Conformation dependent library (CDL) restraints added in 311.0 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: 1.55 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: 1.85 Time building geometry restraints manager: 1.27 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' DT I 15 " pdb=" C2' DT I 15 " ideal model delta sigma weight residual 1.516 1.561 -0.045 8.00e-03 1.56e+04 3.23e+01 bond pdb=" C3' DT I 69 " pdb=" O3' DT I 69 " ideal model delta sigma weight residual 1.435 1.368 0.067 1.30e-02 5.92e+03 2.64e+01 bond pdb=" C2 DC I 61 " pdb=" O2 DC I 61 " ideal model delta sigma weight residual 1.240 1.196 0.044 9.00e-03 1.23e+04 2.40e+01 bond pdb=" C3' DC J 35 " pdb=" C2' DC J 35 " ideal model delta sigma weight residual 1.516 1.555 -0.039 8.00e-03 1.56e+04 2.32e+01 bond pdb=" C3' DT I 67 " pdb=" O3' DT I 67 " ideal model delta sigma weight residual 1.435 1.372 0.063 1.30e-02 5.92e+03 2.32e+01 ... (remaining 12795 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 16953 2.13 - 4.26: 1454 4.26 - 6.40: 126 6.40 - 8.53: 18 8.53 - 10.66: 4 Bond angle restraints: 18555 Sorted by residual: angle pdb=" O4' DG I 4 " pdb=" C1' DG I 4 " pdb=" N9 DG I 4 " ideal model delta sigma weight residual 108.00 114.63 -6.63 7.00e-01 2.04e+00 8.97e+01 angle pdb=" O4' DC I -26 " pdb=" C1' DC I -26 " pdb=" N1 DC I -26 " ideal model delta sigma weight residual 108.00 101.87 6.13 7.00e-01 2.04e+00 7.68e+01 angle pdb=" O4' DC I -28 " pdb=" C1' DC I -28 " pdb=" N1 DC I -28 " ideal model delta sigma weight residual 108.00 102.36 5.64 7.00e-01 2.04e+00 6.50e+01 angle pdb=" O4' DT I 15 " pdb=" C1' DT I 15 " pdb=" N1 DT I 15 " ideal model delta sigma weight residual 108.00 102.54 5.46 7.00e-01 2.04e+00 6.08e+01 angle pdb=" O4' DG I 20 " pdb=" C1' DG I 20 " pdb=" N9 DG I 20 " ideal model delta sigma weight residual 108.00 113.33 -5.33 7.00e-01 2.04e+00 5.80e+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 - 0.090: 1675 0.090 - 0.180: 416 0.180 - 0.271: 26 0.271 - 0.361: 2 0.361 - 0.451: 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 2.43 1.98 0.45 2.00e-01 2.50e+01 5.08e+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 2.43 2.11 0.32 2.00e-01 2.50e+01 2.57e+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 2.43 2.15 0.28 2.00e-01 2.50e+01 1.92e+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: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.130 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 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 0.073 12800 Z= 0.834 Angle : 1.201 10.662 18555 Z= 0.949 Chirality : 0.073 0.451 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/Z covalent geometry : bond 0.00923 / 0.83 (12800) covalent geometry : angle 1.20065 / 0.95 (18555) hydrogen bonds : bond 0.13524 / 9.58 ( 771) hydrogen bonds : angle 5.78257 / 4.14 ( 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 : 0.320 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: 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: 0.5845 (mt) REVERT: A 93 GLN cc_start: 0.8110 (tt0) cc_final: 0.7803 (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: 0.6078 (mtp) REVERT: A 124 ILE cc_start: 0.9470 (mt) cc_final: 0.8923 (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: 0.9068 (t) REVERT: B 88 TYR cc_start: 0.8315 (m-10) cc_final: 0.7670 (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: 0.8889 (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: 0.8115 (t0) REVERT: C 113 SER cc_start: 0.8820 (m) cc_final: 0.8585 (p) REVERT: D 34 TYR cc_start: 0.8699 (m-80) cc_final: 0.8442 (m-10) REVERT: D 41 VAL cc_start: 0.9538 (t) cc_final: 0.9324 (t) REVERT: D 51 ILE cc_start: 0.8376 (pt) cc_final: 0.8031 (tt) REVERT: D 73 GLU cc_start: 0.9177 (mm-30) cc_final: 0.8397 (tt0) REVERT: D 91 ILE cc_start: 0.9697 (mm) cc_final: 0.9495 (pt) REVERT: E 50 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7944 (mt-10) REVERT: E 82 LEU cc_start: 0.5668 (mt) cc_final: 0.5357 (mt) REVERT: E 92 LEU cc_start: 0.9246 (mt) cc_final: 0.8992 (mt) REVERT: E 93 GLN cc_start: 0.8743 (tt0) cc_final: 0.7597 (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: 0.5324 (m-40) REVERT: F 44 LYS cc_start: 0.7914 (tttt) cc_final: 0.7448 (tmmt) REVERT: F 60 VAL cc_start: 0.9127 (t) cc_final: 0.8879 (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: 0.7770 (m-10) REVERT: G 35 ARG cc_start: 0.8699 (mtm180) cc_final: 0.8276 (mtp180) REVERT: G 64 GLU cc_start: 0.9425 (tt0) cc_final: 0.9135 (tp30) REVERT: G 94 ASN cc_start: 0.8753 (t0) cc_final: 0.8496 (t0) REVERT: H 34 TYR cc_start: 0.8028 (m-80) cc_final: 0.7802 (m-10) REVERT: H 37 TYR cc_start: 0.7736 (m-80) cc_final: 0.7451 (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: 0.1349 time to fit residues: 56.2644 Evaluate side-chains 167 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 165 time to evaluate : 0.326 ------------------------------------------------------------------------------- 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: 30.0000 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 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: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 D 106 HIS E 55 GLN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN F 27 GLN G 104 GLN H 46 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.056534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.048921 restraints weight = 107732.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.050228 restraints weight = 65702.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.051127 restraints weight = 44512.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.051791 restraints weight = 32487.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.052237 restraints weight = 25193.851| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 12800 Z= 0.236 Angle : 0.909 12.124 18555 Z= 0.505 Chirality : 0.055 0.340 2120 Planarity : 0.006 0.053 1326 Dihedral : 31.656 171.698 4052 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 22.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 4.63 % Allowed : 17.25 % Favored : 78.12 % 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: -0.13 (0.28), residues: 736 helix: 0.51 (0.21), residues: 535 sheet: None (None), residues: 0 loop : -1.56 (0.38), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 52 TYR 0.028 0.003 TYR G 57 PHE 0.021 0.003 PHE B 61 HIS 0.007 0.002 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.24 (12800) covalent geometry : angle 0.90912 / 0.50 (18555) hydrogen bonds : bond 0.08664 / 5.84 ( 771) hydrogen bonds : angle 4.56683 / 3.31 ( 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 216 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 0.305 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: A 90 MET cc_start: 0.8743 (mmt) cc_final: 0.8515 (mmt) REVERT: A 94 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8457 (mm-30) REVERT: A 120 MET cc_start: 0.6995 (mtp) cc_final: 0.6559 (mtp) REVERT: B 84 MET cc_start: 0.8614 (mpp) cc_final: 0.8224 (mpp) REVERT: B 88 TYR cc_start: 0.8438 (m-10) cc_final: 0.7808 (m-80) REVERT: C 61 GLU cc_start: 0.9181 (tp30) cc_final: 0.8879 (tm-30) REVERT: D 73 GLU cc_start: 0.8995 (mm-30) cc_final: 0.8687 (tp30) REVERT: D 102 GLU cc_start: 0.9252 (tp30) cc_final: 0.8999 (tp30) REVERT: E 93 GLN cc_start: 0.8262 (tt0) cc_final: 0.7837 (tp-100) REVERT: E 104 PHE cc_start: 0.9427 (m-10) cc_final: 0.9096 (m-80) REVERT: E 120 MET cc_start: 0.7354 (mtp) cc_final: 0.7144 (mtt) REVERT: F 25 ASN cc_start: 0.5926 (m110) cc_final: 0.5559 (m-40) REVERT: F 44 LYS cc_start: 0.7946 (tttt) cc_final: 0.7529 (ttpt) REVERT: F 59 LYS cc_start: 0.9548 (tttm) cc_final: 0.9195 (tptm) REVERT: F 63 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8245 (mp0) REVERT: F 88 TYR cc_start: 0.8356 (m-10) cc_final: 0.7921 (m-10) REVERT: G 35 ARG cc_start: 0.8530 (mtm180) cc_final: 0.8244 (mtp180) REVERT: G 84 GLN cc_start: 0.8633 (tp40) cc_final: 0.8161 (tm-30) REVERT: G 91 GLU cc_start: 0.9267 (pm20) cc_final: 0.9031 (pm20) REVERT: H 39 TYR cc_start: 0.8637 (OUTLIER) cc_final: 0.8045 (m-80) REVERT: H 73 GLU cc_start: 0.9108 (mm-30) cc_final: 0.8543 (tp30) REVERT: H 106 HIS cc_start: 0.8894 (m-70) cc_final: 0.8330 (m90) outliers start: 29 outliers final: 18 residues processed: 200 average time/residue: 0.1119 time to fit residues: 31.6195 Evaluate side-chains 159 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 51 TYR 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 87 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 97 LEU 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 F residue 63 GLU 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 51 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 113 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 73 optimal weight: 40.0000 chunk 57 optimal weight: 4.9990 chunk 95 optimal weight: 30.0000 chunk 20 optimal weight: 6.9990 chunk 88 optimal weight: 30.0000 chunk 77 optimal weight: 40.0000 chunk 35 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 21 optimal weight: 0.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS ** 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** ** F 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 = 0.3589 r_free = 0.3589 target = 0.055516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.048319 restraints weight = 105908.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.049623 restraints weight = 63473.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.050514 restraints weight = 42391.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.051149 restraints weight = 30617.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.051628 restraints weight = 23569.099| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 12800 Z= 0.227 Angle : 0.835 11.366 18555 Z= 0.470 Chirality : 0.053 0.307 2120 Planarity : 0.006 0.045 1326 Dihedral : 31.844 174.180 4052 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 23.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.99 % Allowed : 19.97 % Favored : 76.04 % 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: -0.08 (0.29), residues: 736 helix: 0.65 (0.21), residues: 535 sheet: None (None), residues: 0 loop : -1.87 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 29 TYR 0.028 0.003 TYR H 37 PHE 0.021 0.003 PHE B 61 HIS 0.006 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.23 (12800) covalent geometry : angle 0.83504 / 0.47 (18555) hydrogen bonds : bond 0.08859 / 5.98 ( 771) hydrogen bonds : angle 4.48674 / 3.24 ( 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 177 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 0.334 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: B 88 TYR cc_start: 0.8537 (m-10) cc_final: 0.7883 (m-80) REVERT: C 61 GLU cc_start: 0.9183 (tp30) cc_final: 0.8854 (tm-30) REVERT: D 73 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8773 (tp30) REVERT: D 102 GLU cc_start: 0.9171 (tp30) cc_final: 0.8660 (tm-30) REVERT: D 106 HIS cc_start: 0.8408 (m90) cc_final: 0.7822 (m-70) REVERT: E 55 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.8389 (tm-30) REVERT: E 93 GLN cc_start: 0.8204 (tt0) cc_final: 0.7692 (tp-100) REVERT: F 25 ASN cc_start: 0.6047 (m110) cc_final: 0.5670 (m-40) REVERT: F 44 LYS cc_start: 0.8178 (tttt) cc_final: 0.7716 (ttpt) REVERT: F 88 TYR cc_start: 0.8460 (m-10) cc_final: 0.8013 (m-10) REVERT: G 94 ASN cc_start: 0.8497 (OUTLIER) cc_final: 0.8228 (m-40) REVERT: H 34 TYR cc_start: 0.8082 (m-80) cc_final: 0.7670 (m-80) REVERT: H 39 TYR cc_start: 0.8576 (OUTLIER) cc_final: 0.7882 (m-80) REVERT: H 73 GLU cc_start: 0.9106 (mm-30) cc_final: 0.8601 (tp30) REVERT: H 102 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8245 (tm-30) REVERT: H 103 LEU cc_start: 0.9540 (mt) cc_final: 0.9044 (mt) REVERT: H 106 HIS cc_start: 0.8961 (m-70) cc_final: 0.8490 (m90) outliers start: 25 outliers final: 14 residues processed: 168 average time/residue: 0.1017 time to fit residues: 25.3040 Evaluate side-chains 143 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain B residue 21 VAL 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 36 ILE Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 55 GLN Chi-restraints excluded: chain F residue 51 TYR 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 39 TYR Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 102 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 60 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 86 optimal weight: 50.0000 chunk 98 optimal weight: 40.0000 chunk 8 optimal weight: 5.9990 chunk 71 optimal weight: 50.0000 chunk 14 optimal weight: 6.9990 chunk 82 optimal weight: 40.0000 chunk 87 optimal weight: 40.0000 chunk 48 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.054994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.048150 restraints weight = 109806.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.049325 restraints weight = 68245.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.050117 restraints weight = 46578.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.050721 restraints weight = 34522.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.051155 restraints weight = 26849.004| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 12800 Z= 0.227 Angle : 0.819 10.538 18555 Z= 0.461 Chirality : 0.051 0.294 2120 Planarity : 0.005 0.046 1326 Dihedral : 31.906 171.683 4048 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 24.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 4.47 % Allowed : 19.65 % Favored : 75.88 % 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: -0.20 (0.29), residues: 736 helix: 0.54 (0.21), residues: 535 sheet: None (None), residues: 0 loop : -1.83 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 116 TYR 0.022 0.002 TYR D 37 PHE 0.022 0.003 PHE A 104 HIS 0.006 0.002 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.23 (12800) covalent geometry : angle 0.81924 / 0.46 (18555) hydrogen bonds : bond 0.08848 / 5.97 ( 771) hydrogen bonds : angle 4.37864 / 3.18 ( 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 170 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 142 time to evaluate : 0.306 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: B 25 ASN cc_start: 0.5736 (m110) cc_final: 0.5412 (m110) REVERT: B 88 TYR cc_start: 0.8583 (m-10) cc_final: 0.7892 (m-80) REVERT: C 61 GLU cc_start: 0.9020 (tp30) cc_final: 0.8749 (tm-30) REVERT: D 73 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8560 (tp30) REVERT: D 102 GLU cc_start: 0.8951 (tp30) cc_final: 0.8379 (tm-30) REVERT: D 106 HIS cc_start: 0.8060 (m90) cc_final: 0.7404 (m90) REVERT: E 93 GLN cc_start: 0.8103 (tt0) cc_final: 0.7167 (tp40) REVERT: E 97 GLU cc_start: 0.7480 (mt-10) cc_final: 0.6406 (mt-10) REVERT: F 25 ASN cc_start: 0.6106 (m110) cc_final: 0.5703 (m-40) REVERT: F 63 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7891 (mp0) REVERT: F 88 TYR cc_start: 0.8467 (m-10) cc_final: 0.7962 (m-10) REVERT: G 94 ASN cc_start: 0.8353 (OUTLIER) cc_final: 0.7830 (m110) REVERT: H 39 TYR cc_start: 0.8278 (OUTLIER) cc_final: 0.7555 (m-80) REVERT: H 73 GLU cc_start: 0.8961 (mm-30) cc_final: 0.8396 (tp30) REVERT: H 77 LEU cc_start: 0.8965 (mm) cc_final: 0.8709 (mm) REVERT: H 102 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8191 (tm-30) REVERT: H 103 LEU cc_start: 0.9463 (mt) cc_final: 0.9244 (mt) REVERT: H 106 HIS cc_start: 0.8642 (m-70) cc_final: 0.8314 (m90) outliers start: 28 outliers final: 20 residues processed: 158 average time/residue: 0.0955 time to fit residues: 22.7114 Evaluate side-chains 148 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 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 B residue 34 ILE 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 43 VAL 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 D residue 97 LEU 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 F residue 51 TYR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 TYR Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 102 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 84 optimal weight: 40.0000 chunk 8 optimal weight: 0.8980 chunk 17 optimal weight: 20.0000 chunk 26 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 34 optimal weight: 0.8980 chunk 36 optimal weight: 30.0000 chunk 77 optimal weight: 40.0000 chunk 60 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 3 optimal weight: 9.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 94 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.056013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.049149 restraints weight = 113744.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.050310 restraints weight = 70731.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.051098 restraints weight = 48343.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.051685 restraints weight = 35871.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.052082 restraints weight = 28085.900| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 12800 Z= 0.187 Angle : 0.776 9.104 18555 Z= 0.439 Chirality : 0.050 0.284 2120 Planarity : 0.005 0.044 1326 Dihedral : 31.889 171.321 4048 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 22.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.63 % Allowed : 21.09 % Favored : 74.28 % 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: -0.26 (0.29), residues: 736 helix: 0.50 (0.21), residues: 537 sheet: None (None), residues: 0 loop : -1.88 (0.37), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 55 TYR 0.014 0.002 TYR D 37 PHE 0.018 0.003 PHE D 62 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.19 (12800) covalent geometry : angle 0.77612 / 0.44 (18555) hydrogen bonds : bond 0.07298 / 4.87 ( 771) hydrogen bonds : angle 4.23579 / 3.09 ( 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: 29 poor density : 144 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: A 90 MET cc_start: 0.8664 (mmm) cc_final: 0.8462 (mmm) REVERT: B 25 ASN cc_start: 0.5494 (m110) cc_final: 0.5111 (m110) REVERT: B 88 TYR cc_start: 0.8540 (m-10) cc_final: 0.7884 (m-80) REVERT: C 61 GLU cc_start: 0.9022 (tp30) cc_final: 0.8627 (tm-30) REVERT: C 94 ASN cc_start: 0.8419 (OUTLIER) cc_final: 0.7882 (m-40) REVERT: D 39 TYR cc_start: 0.8555 (OUTLIER) cc_final: 0.7713 (m-80) REVERT: D 73 GLU cc_start: 0.8894 (mm-30) cc_final: 0.8521 (tp30) REVERT: D 102 GLU cc_start: 0.9006 (tp30) cc_final: 0.8412 (tm-30) REVERT: D 106 HIS cc_start: 0.8091 (m90) cc_final: 0.7443 (m90) REVERT: E 93 GLN cc_start: 0.8178 (tt0) cc_final: 0.7119 (tp-100) REVERT: E 97 GLU cc_start: 0.7531 (mt-10) cc_final: 0.5891 (mt-10) REVERT: F 25 ASN cc_start: 0.5994 (m110) cc_final: 0.5532 (m-40) REVERT: F 84 MET cc_start: 0.8654 (mpp) cc_final: 0.8424 (mmm) REVERT: F 88 TYR cc_start: 0.8507 (m-10) cc_final: 0.8023 (m-10) REVERT: F 100 PHE cc_start: 0.7637 (m-80) cc_final: 0.6961 (m-80) REVERT: H 39 TYR cc_start: 0.8353 (OUTLIER) cc_final: 0.7616 (m-80) REVERT: H 73 GLU cc_start: 0.8982 (mm-30) cc_final: 0.8357 (tp30) REVERT: H 77 LEU cc_start: 0.8956 (mm) cc_final: 0.8648 (mm) REVERT: H 102 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8333 (tm-30) REVERT: H 106 HIS cc_start: 0.8589 (m-70) cc_final: 0.8225 (m-70) outliers start: 29 outliers final: 19 residues processed: 163 average time/residue: 0.0950 time to fit residues: 23.2847 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 : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 39 TYR 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 55 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 TYR Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 102 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 93 optimal weight: 40.0000 chunk 68 optimal weight: 0.0000 chunk 15 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 77 optimal weight: 30.0000 chunk 60 optimal weight: 0.9990 chunk 17 optimal weight: 20.0000 chunk 73 optimal weight: 40.0000 chunk 13 optimal weight: 5.9990 overall best weight: 3.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 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 = 0.3605 r_free = 0.3605 target = 0.055834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.048776 restraints weight = 113365.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.049961 restraints weight = 70186.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.050807 restraints weight = 48139.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.051399 restraints weight = 35450.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.051820 restraints weight = 27738.349| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 12800 Z= 0.188 Angle : 0.764 8.028 18555 Z= 0.436 Chirality : 0.049 0.273 2120 Planarity : 0.005 0.049 1326 Dihedral : 31.866 170.361 4048 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 24.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.63 % Allowed : 23.96 % Favored : 71.41 % 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: -0.30 (0.29), residues: 736 helix: 0.49 (0.21), residues: 539 sheet: None (None), residues: 0 loop : -1.99 (0.36), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 63 TYR 0.026 0.002 TYR D 37 PHE 0.023 0.003 PHE G 25 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.19 (12800) covalent geometry : angle 0.76362 / 0.44 (18555) hydrogen bonds : bond 0.07446 / 4.95 ( 771) hydrogen bonds : angle 4.23506 / 3.09 ( 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 163 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 0.310 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: B 25 ASN cc_start: 0.5503 (m110) cc_final: 0.5133 (m110) REVERT: B 88 TYR cc_start: 0.8559 (m-10) cc_final: 0.7896 (m-80) REVERT: C 61 GLU cc_start: 0.8950 (tp30) cc_final: 0.8591 (tm-30) REVERT: D 39 TYR cc_start: 0.8537 (OUTLIER) cc_final: 0.7670 (m-80) REVERT: D 51 ILE cc_start: 0.7985 (pt) cc_final: 0.7170 (tt) REVERT: D 73 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8501 (tp30) REVERT: D 102 GLU cc_start: 0.8964 (tp30) cc_final: 0.8349 (tm-30) REVERT: D 106 HIS cc_start: 0.8017 (m90) cc_final: 0.7359 (m90) REVERT: E 93 GLN cc_start: 0.8234 (tt0) cc_final: 0.7186 (tt0) REVERT: E 97 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7454 (mt-10) REVERT: F 25 ASN cc_start: 0.6000 (m110) cc_final: 0.5538 (m-40) REVERT: F 88 TYR cc_start: 0.8475 (m-10) cc_final: 0.7965 (m-10) REVERT: H 39 TYR cc_start: 0.8263 (OUTLIER) cc_final: 0.7566 (m-80) REVERT: H 73 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8371 (tp30) REVERT: H 77 LEU cc_start: 0.8940 (mm) cc_final: 0.8644 (mm) REVERT: H 102 GLU cc_start: 0.9016 (OUTLIER) cc_final: 0.8354 (tm-30) REVERT: H 106 HIS cc_start: 0.8571 (m-70) cc_final: 0.8198 (m-70) outliers start: 29 outliers final: 20 residues processed: 153 average time/residue: 0.0911 time to fit residues: 21.2245 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 : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 34 ILE 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 39 TYR 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 55 GLN Chi-restraints excluded: chain E residue 80 THR 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 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 TYR Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 102 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 39 optimal weight: 5.9990 chunk 47 optimal weight: 20.0000 chunk 55 optimal weight: 9.9990 chunk 33 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 80 optimal weight: 20.0000 chunk 90 optimal weight: 50.0000 chunk 98 optimal weight: 40.0000 chunk 14 optimal weight: 0.8980 chunk 79 optimal weight: 30.0000 chunk 42 optimal weight: 0.8980 overall best weight: 2.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 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** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.056251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.049249 restraints weight = 108282.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.050451 restraints weight = 67287.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.051297 restraints weight = 46044.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.051897 restraints weight = 33896.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.052291 restraints weight = 26511.810| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 12800 Z= 0.173 Angle : 0.751 10.588 18555 Z= 0.426 Chirality : 0.049 0.273 2120 Planarity : 0.005 0.049 1326 Dihedral : 31.826 169.487 4048 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 23.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.99 % Allowed : 25.24 % Favored : 70.77 % 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: -0.22 (0.29), residues: 736 helix: 0.58 (0.22), residues: 539 sheet: None (None), residues: 0 loop : -2.08 (0.36), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 131 TYR 0.020 0.002 TYR D 37 PHE 0.021 0.002 PHE G 25 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.17 (12800) covalent geometry : angle 0.75103 / 0.43 (18555) hydrogen bonds : bond 0.06697 / 4.41 ( 771) hydrogen bonds : angle 4.12333 / 3.02 ( 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 171 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 146 time to evaluate : 0.444 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: B 25 ASN cc_start: 0.5548 (m110) cc_final: 0.5224 (m110) REVERT: B 88 TYR cc_start: 0.8553 (m-10) cc_final: 0.7909 (m-80) REVERT: C 61 GLU cc_start: 0.8969 (tp30) cc_final: 0.8630 (tm-30) REVERT: D 39 TYR cc_start: 0.8490 (OUTLIER) cc_final: 0.7593 (m-80) REVERT: D 51 ILE cc_start: 0.8107 (pt) cc_final: 0.7033 (tt) REVERT: D 73 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8475 (tp30) REVERT: D 102 GLU cc_start: 0.8955 (tp30) cc_final: 0.8330 (tm-30) REVERT: D 106 HIS cc_start: 0.8008 (m90) cc_final: 0.7347 (m90) REVERT: E 93 GLN cc_start: 0.8236 (tt0) cc_final: 0.7181 (tt0) REVERT: E 97 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7474 (mt-10) REVERT: F 25 ASN cc_start: 0.5906 (m110) cc_final: 0.5465 (m-40) REVERT: F 88 TYR cc_start: 0.8529 (m-10) cc_final: 0.8037 (m-10) REVERT: G 94 ASN cc_start: 0.8134 (OUTLIER) cc_final: 0.7500 (m110) REVERT: G 113 SER cc_start: 0.8563 (m) cc_final: 0.8356 (m) REVERT: H 43 LYS cc_start: 0.9274 (tptp) cc_final: 0.9072 (tppt) REVERT: H 73 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8485 (tp30) REVERT: H 102 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8377 (tm-30) REVERT: H 103 LEU cc_start: 0.9375 (mt) cc_final: 0.9122 (mt) REVERT: H 106 HIS cc_start: 0.8649 (m-70) cc_final: 0.7964 (m170) outliers start: 25 outliers final: 18 residues processed: 162 average time/residue: 0.0963 time to fit residues: 23.9284 Evaluate side-chains 155 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 34 ILE 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 39 TYR 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 55 GLN Chi-restraints excluded: chain E residue 80 THR 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 94 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 102 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 57 optimal weight: 5.9990 chunk 77 optimal weight: 30.0000 chunk 40 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 91 optimal weight: 30.0000 chunk 28 optimal weight: 6.9990 chunk 44 optimal weight: 0.4980 chunk 31 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 11 optimal weight: 20.0000 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 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** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.057101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.050007 restraints weight = 112388.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.051209 restraints weight = 69811.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.052027 restraints weight = 47752.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.052636 restraints weight = 35355.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.053050 restraints weight = 27718.029| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 12800 Z= 0.164 Angle : 0.755 12.546 18555 Z= 0.424 Chirality : 0.048 0.271 2120 Planarity : 0.005 0.050 1326 Dihedral : 31.755 168.912 4048 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 22.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.19 % Allowed : 27.32 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.29), residues: 736 helix: 0.55 (0.22), residues: 537 sheet: None (None), residues: 0 loop : -2.14 (0.35), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 131 TYR 0.024 0.002 TYR H 37 PHE 0.018 0.002 PHE D 62 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.16 (12800) covalent geometry : angle 0.75452 / 0.42 (18555) hydrogen bonds : bond 0.06302 / 4.13 ( 771) hydrogen bonds : angle 4.10238 / 3.00 ( 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 171 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 0.307 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: B 25 ASN cc_start: 0.5511 (m110) cc_final: 0.5180 (m110) REVERT: B 88 TYR cc_start: 0.8543 (m-10) cc_final: 0.7914 (m-80) REVERT: C 61 GLU cc_start: 0.9070 (tp30) cc_final: 0.8659 (tm-30) REVERT: D 39 TYR cc_start: 0.8558 (OUTLIER) cc_final: 0.7837 (m-80) REVERT: D 56 MET cc_start: 0.7079 (tpt) cc_final: 0.6593 (tpt) REVERT: D 73 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8477 (tp30) REVERT: D 102 GLU cc_start: 0.8974 (tp30) cc_final: 0.8413 (tm-30) REVERT: D 106 HIS cc_start: 0.7991 (m90) cc_final: 0.7412 (m90) REVERT: E 93 GLN cc_start: 0.8194 (tt0) cc_final: 0.7089 (tt0) REVERT: F 25 ASN cc_start: 0.5916 (m110) cc_final: 0.5486 (m-40) REVERT: F 88 TYR cc_start: 0.8448 (m-10) cc_final: 0.7938 (m-10) REVERT: G 94 ASN cc_start: 0.8397 (t0) cc_final: 0.8030 (m-40) REVERT: H 73 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8437 (tp30) REVERT: H 102 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8211 (tm-30) REVERT: H 103 LEU cc_start: 0.9322 (mt) cc_final: 0.9107 (mt) REVERT: H 106 HIS cc_start: 0.8602 (m-70) cc_final: 0.7929 (m-70) outliers start: 20 outliers final: 17 residues processed: 164 average time/residue: 0.0903 time to fit residues: 22.5242 Evaluate side-chains 155 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 34 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 39 TYR 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 123 ASP 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 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 102 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 89 optimal weight: 40.0000 chunk 48 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 7 optimal weight: 9.9990 chunk 81 optimal weight: 30.0000 chunk 52 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 87 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 28 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN ** F 93 GLN ** 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 = 0.3614 r_free = 0.3614 target = 0.056195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.049153 restraints weight = 112128.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.050326 restraints weight = 70466.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.051125 restraints weight = 48542.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.051719 restraints weight = 36097.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.052131 restraints weight = 28366.814| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 12800 Z= 0.187 Angle : 0.790 14.545 18555 Z= 0.439 Chirality : 0.049 0.270 2120 Planarity : 0.005 0.048 1326 Dihedral : 31.701 168.491 4048 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 24.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.67 % Allowed : 27.00 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.29), residues: 736 helix: 0.38 (0.22), residues: 537 sheet: None (None), residues: 0 loop : -2.16 (0.36), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 36 TYR 0.015 0.002 TYR H 37 PHE 0.021 0.003 PHE C 25 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.19 (12800) covalent geometry : angle 0.79012 / 0.44 (18555) hydrogen bonds : bond 0.07220 / 4.74 ( 771) hydrogen bonds : angle 4.30490 / 3.11 ( 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 162 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.277 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: B 25 ASN cc_start: 0.5514 (m110) cc_final: 0.5190 (m110) REVERT: B 88 TYR cc_start: 0.8595 (m-10) cc_final: 0.7975 (m-80) REVERT: C 61 GLU cc_start: 0.9076 (tp30) cc_final: 0.8659 (tm-30) REVERT: C 64 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7973 (mm-30) REVERT: D 39 TYR cc_start: 0.8640 (OUTLIER) cc_final: 0.7785 (m-80) REVERT: D 56 MET cc_start: 0.7305 (tpt) cc_final: 0.6693 (tpt) REVERT: D 73 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8509 (tp30) REVERT: D 102 GLU cc_start: 0.8929 (tp30) cc_final: 0.8310 (tm-30) REVERT: D 106 HIS cc_start: 0.7966 (m90) cc_final: 0.7368 (m90) REVERT: F 25 ASN cc_start: 0.5977 (m110) cc_final: 0.5576 (m-40) REVERT: F 88 TYR cc_start: 0.8497 (m-10) cc_final: 0.7992 (m-10) REVERT: G 56 GLU cc_start: 0.9122 (tt0) cc_final: 0.8768 (tt0) REVERT: G 113 SER cc_start: 0.8536 (m) cc_final: 0.8334 (m) REVERT: H 73 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8465 (tp30) REVERT: H 102 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.8338 (tm-30) REVERT: H 106 HIS cc_start: 0.8630 (m-70) cc_final: 0.7898 (m-70) outliers start: 23 outliers final: 19 residues processed: 156 average time/residue: 0.0847 time to fit residues: 20.3300 Evaluate side-chains 154 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 CYS 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 34 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 39 TYR Chi-restraints excluded: chain D residue 85 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 E residue 123 ASP 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 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 102 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 87 optimal weight: 40.0000 chunk 53 optimal weight: 20.0000 chunk 80 optimal weight: 30.0000 chunk 2 optimal weight: 5.9990 chunk 47 optimal weight: 20.0000 chunk 61 optimal weight: 6.9990 chunk 84 optimal weight: 40.0000 chunk 91 optimal weight: 40.0000 chunk 92 optimal weight: 30.0000 chunk 25 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 overall best weight: 8.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.052626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.045753 restraints weight = 116671.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.046896 restraints weight = 71872.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.047662 restraints weight = 48835.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.048239 restraints weight = 36088.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.048633 restraints weight = 28117.501| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.5050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 12800 Z= 0.301 Angle : 0.912 14.717 18555 Z= 0.508 Chirality : 0.054 0.289 2120 Planarity : 0.007 0.052 1326 Dihedral : 31.874 168.768 4048 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 36.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.51 % Allowed : 27.80 % Favored : 68.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.28), residues: 736 helix: -0.27 (0.21), residues: 535 sheet: None (None), residues: 0 loop : -2.14 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 131 TYR 0.020 0.003 TYR D 118 PHE 0.022 0.004 PHE D 62 HIS 0.009 0.003 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.30 (12800) covalent geometry : angle 0.91248 / 0.51 (18555) hydrogen bonds : bond 0.12667 / 8.53 ( 771) hydrogen bonds : angle 4.90042 / 3.53 ( 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 152 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 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: B 25 ASN cc_start: 0.5542 (m110) cc_final: 0.5166 (m110) REVERT: B 44 LYS cc_start: 0.8074 (mtpt) cc_final: 0.7813 (mtpp) REVERT: B 88 TYR cc_start: 0.8659 (m-10) cc_final: 0.8102 (m-80) REVERT: C 25 PHE cc_start: 0.7708 (m-80) cc_final: 0.7115 (m-80) REVERT: C 56 GLU cc_start: 0.9245 (tt0) cc_final: 0.8711 (tt0) REVERT: C 61 GLU cc_start: 0.9158 (tp30) cc_final: 0.8699 (tm-30) REVERT: C 64 GLU cc_start: 0.8397 (mm-30) cc_final: 0.7895 (mm-30) REVERT: D 39 TYR cc_start: 0.8597 (OUTLIER) cc_final: 0.7593 (m-80) REVERT: D 73 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8668 (tp30) REVERT: D 106 HIS cc_start: 0.8215 (m90) cc_final: 0.7789 (m90) REVERT: E 93 GLN cc_start: 0.7945 (tt0) cc_final: 0.7649 (tp40) REVERT: F 25 ASN cc_start: 0.6187 (m110) cc_final: 0.5670 (m-40) REVERT: F 88 TYR cc_start: 0.8616 (m-10) cc_final: 0.8064 (m-80) REVERT: G 56 GLU cc_start: 0.9155 (tt0) cc_final: 0.8821 (tt0) REVERT: H 73 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8396 (tp30) REVERT: H 102 GLU cc_start: 0.9130 (OUTLIER) cc_final: 0.8644 (tm-30) REVERT: H 106 HIS cc_start: 0.8586 (m-70) cc_final: 0.8156 (m-70) outliers start: 22 outliers final: 18 residues processed: 146 average time/residue: 0.0977 time to fit residues: 21.6181 Evaluate side-chains 145 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 CYS 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 34 ILE 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 39 TYR 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 123 ASP Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 102 GLU 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: 6.9990 chunk 21 optimal weight: 5.9990 chunk 81 optimal weight: 30.0000 chunk 97 optimal weight: 40.0000 chunk 10 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 84 optimal weight: 40.0000 chunk 85 optimal weight: 40.0000 chunk 66 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.054627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.047882 restraints weight = 115760.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.049019 restraints weight = 71730.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.049824 restraints weight = 49111.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.050392 restraints weight = 36180.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.050772 restraints weight = 28348.798| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.5079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 12800 Z= 0.196 Angle : 0.822 13.939 18555 Z= 0.457 Chirality : 0.051 0.279 2120 Planarity : 0.005 0.048 1326 Dihedral : 31.996 169.488 4048 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 25.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.51 % Allowed : 28.43 % Favored : 68.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.29), residues: 736 helix: -0.05 (0.21), residues: 537 sheet: None (None), residues: 0 loop : -2.21 (0.37), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 52 TYR 0.022 0.002 TYR D 37 PHE 0.019 0.002 PHE D 62 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.20 (12800) covalent geometry : angle 0.82214 / 0.46 (18555) hydrogen bonds : bond 0.07506 / 4.96 ( 771) hydrogen bonds : angle 4.53214 / 3.28 ( 1911) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1632.74 seconds wall clock time: 29 minutes 8.80 seconds (1748.80 seconds total)