Starting phenix.real_space_refine on Thu Aug 6 00:35:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8peo_17633/08_2026/8peo_17633.cif Found real_map, /net/cci-nas-00/data/ceres_data/8peo_17633/08_2026/8peo_17633.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8peo_17633/08_2026/8peo_17633.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8peo_17633/08_2026/8peo_17633.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8peo_17633/08_2026/8peo_17633.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8peo_17633/08_2026/8peo_17633.cif" model { file = "/net/cci-nas-00/data/ceres_data/8peo_17633/08_2026/8peo_17633.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8peo_17633/08_2026/8peo_17633.cif" } resolution = 2.69 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= 0.001 sd= 0.013 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 13 5.16 5 C 7171 2.51 5 N 2399 2.21 5 O 2958 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12835 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 817 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain breaks: 1 Chain: "B" 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: "C" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 694 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "G" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 710 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 11, 'TRANS': 74} Chain breaks: 1 Chain: "J" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M2L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 2.38, per 1000 atoms: 0.19 Number of scatterers: 12835 At special positions: 0 Unit cell: (91.696, 119.205, 138.378, 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 13 16.00 P 294 15.00 O 2958 8.00 N 2399 7.00 C 7171 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 291.0 milliseconds 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1598 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 11 sheets defined 64.5% alpha, 4.8% beta 146 base pairs and 270 stacking pairs defined. Time for finding SS restraints: 1.86 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.569A pdb=" N ALA A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.613A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.858A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.569A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 removed outlier: 3.807A pdb=" N ARG C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.575A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 121 removed outlier: 3.801A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 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: 3.508A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.794A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.602A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.397A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 removed outlier: 4.112A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.720A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.477A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.143A 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 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.343A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.210A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 49 through 53 removed outlier: 3.839A pdb=" N GLU K 49 " --> pdb=" O PHE K 44 " (cutoff:3.500A) 411 hydrogen bonds defined for protein. 1212 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 374 hydrogen bonds 748 hydrogen bond angles 0 basepair planarities 146 basepair parallelities 270 stacking parallelities Total time for adding SS restraints: 2.18 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2228 1.33 - 1.45: 4599 1.45 - 1.57: 6234 1.57 - 1.69: 586 1.69 - 1.82: 26 Bond restraints: 13673 Sorted by residual: bond pdb=" C3' DC J -71 " pdb=" C2' DC J -71 " ideal model delta sigma weight residual 1.516 1.548 -0.032 8.00e-03 1.56e+04 1.65e+01 bond pdb=" C3' DG I -61 " pdb=" C2' DG I -61 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.29e+01 bond pdb=" C1' DC I -62 " pdb=" N1 DC I -62 " ideal model delta sigma weight residual 1.468 1.514 -0.046 1.40e-02 5.10e+03 1.06e+01 bond pdb=" C3' DG J 64 " pdb=" C2' DG J 64 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C3' DC I 33 " pdb=" C2' DC I 33 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.95e+00 ... (remaining 13668 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 18231 1.76 - 3.52: 1367 3.52 - 5.28: 101 5.28 - 7.03: 17 7.03 - 8.79: 5 Bond angle restraints: 19721 Sorted by residual: angle pdb=" O5' DA J -62 " pdb=" C5' DA J -62 " pdb=" C4' DA J -62 " ideal model delta sigma weight residual 109.40 113.72 -4.32 8.00e-01 1.56e+00 2.91e+01 angle pdb=" O5' DA I 67 " pdb=" C5' DA I 67 " pdb=" C4' DA I 67 " ideal model delta sigma weight residual 109.40 113.46 -4.06 8.00e-01 1.56e+00 2.57e+01 angle pdb=" O4' DT J -72 " pdb=" C1' DT J -72 " pdb=" N1 DT J -72 " ideal model delta sigma weight residual 108.00 111.46 -3.46 7.00e-01 2.04e+00 2.45e+01 angle pdb=" O5' DG J 23 " pdb=" C5' DG J 23 " pdb=" C4' DG J 23 " ideal model delta sigma weight residual 109.40 113.26 -3.86 8.00e-01 1.56e+00 2.33e+01 angle pdb=" O4' DA I 67 " pdb=" C4' DA I 67 " pdb=" C3' DA I 67 " ideal model delta sigma weight residual 106.00 103.17 2.83 6.00e-01 2.78e+00 2.23e+01 ... (remaining 19716 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.44: 5770 35.44 - 70.87: 1661 70.87 - 106.31: 37 106.31 - 141.74: 3 141.74 - 177.18: 4 Dihedral angle restraints: 7475 sinusoidal: 5003 harmonic: 2472 Sorted by residual: dihedral pdb=" CD M2L A 201 " pdb=" CE M2L A 201 " pdb=" NZ M2L A 201 " pdb=" CM1 M2L A 201 " ideal model delta sinusoidal sigma weight residual 66.23 -97.71 163.94 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C4' DT J 69 " pdb=" C3' DT J 69 " pdb=" O3' DT J 69 " pdb=" P DC J 70 " ideal model delta sinusoidal sigma weight residual 220.00 42.82 177.18 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC J 68 " pdb=" C3' DC J 68 " pdb=" O3' DC J 68 " pdb=" P DT J 69 " ideal model delta sinusoidal sigma weight residual -140.00 24.39 -164.39 1 3.50e+01 8.16e-04 1.54e+01 ... (remaining 7472 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 2156 0.106 - 0.213: 68 0.213 - 0.319: 1 0.319 - 0.425: 0 0.425 - 0.531: 4 Chirality restraints: 2229 Sorted by residual: chirality pdb=" P DG J 50 " pdb=" OP1 DG J 50 " pdb=" OP2 DG J 50 " pdb=" O5' DG J 50 " both_signs ideal model delta sigma weight residual True 2.34 -2.87 -0.53 2.00e-01 2.50e+01 7.05e+00 chirality pdb=" P DC J 49 " pdb=" OP1 DC J 49 " pdb=" OP2 DC J 49 " pdb=" O5' DC J 49 " both_signs ideal model delta sigma weight residual True 2.34 -2.86 -0.53 2.00e-01 2.50e+01 6.94e+00 chirality pdb=" P DC I -50 " pdb=" OP1 DC I -50 " pdb=" OP2 DC I -50 " pdb=" O5' DC I -50 " both_signs ideal model delta sigma weight residual True 2.34 -2.86 -0.53 2.00e-01 2.50e+01 6.92e+00 ... (remaining 2226 not shown) Planarity restraints: 1477 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN G 73 " -0.019 2.00e-02 2.50e+03 3.88e-02 1.51e+01 pdb=" C ASN G 73 " 0.067 2.00e-02 2.50e+03 pdb=" O ASN G 73 " -0.025 2.00e-02 2.50e+03 pdb=" N LYS G 74 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 69 " -0.040 2.00e-02 2.50e+03 2.41e-02 1.31e+01 pdb=" N1 DC I 69 " 0.057 2.00e-02 2.50e+03 pdb=" C2 DC I 69 " -0.013 2.00e-02 2.50e+03 pdb=" O2 DC I 69 " 0.009 2.00e-02 2.50e+03 pdb=" N3 DC I 69 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DC I 69 " -0.004 2.00e-02 2.50e+03 pdb=" N4 DC I 69 " -0.010 2.00e-02 2.50e+03 pdb=" C5 DC I 69 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DC I 69 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 49 " 0.030 2.00e-02 2.50e+03 2.39e-02 1.28e+01 pdb=" N1 DC I 49 " -0.057 2.00e-02 2.50e+03 pdb=" C2 DC I 49 " 0.028 2.00e-02 2.50e+03 pdb=" O2 DC I 49 " -0.010 2.00e-02 2.50e+03 pdb=" N3 DC I 49 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DC I 49 " 0.003 2.00e-02 2.50e+03 pdb=" N4 DC I 49 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DC I 49 " 0.006 2.00e-02 2.50e+03 pdb=" C6 DC I 49 " -0.001 2.00e-02 2.50e+03 ... (remaining 1474 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1279 2.74 - 3.28: 10720 3.28 - 3.82: 25198 3.82 - 4.36: 30038 4.36 - 4.90: 43095 Nonbonded interactions: 110330 Sorted by model distance: nonbonded pdb=" O GLU K 66 " pdb=" NZ LYS K 70 " model vdw 2.201 3.120 nonbonded pdb=" N GLU A 59 " pdb=" OE1 GLU A 59 " model vdw 2.204 3.120 nonbonded pdb=" NZ LYS H 43 " pdb=" O THR H 49 " model vdw 2.219 3.120 nonbonded pdb=" O TRP K 82 " pdb=" ND2 ASN K 86 " model vdw 2.241 3.120 nonbonded pdb=" OG1 THR F 73 " pdb=" OD2 ASP F 85 " model vdw 2.254 3.040 ... (remaining 110325 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' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 20 through 101) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 6.390 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: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.850 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 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 : 0.006 0.102 13675 Z= 0.559 Angle : 0.910 8.793 19721 Z= 0.759 Chirality : 0.053 0.531 2229 Planarity : 0.006 0.119 1477 Dihedral : 29.822 177.176 5877 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.14 % Allowed : 20.20 % Favored : 79.66 % 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: 0.99 (0.29), residues: 831 helix: 1.68 (0.22), residues: 548 sheet: -2.59 (0.96), residues: 23 loop : -1.27 (0.34), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 35 TYR 0.013 0.002 TYR F 51 PHE 0.014 0.002 PHE K 5 TRP 0.019 0.003 TRP K 82 HIS 0.007 0.001 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00638 / 0.54 (13673) covalent geometry : angle 0.91048 / 0.76 (19721) hydrogen bonds : bond 0.12696 / 8.63 ( 785) hydrogen bonds : angle 3.94289 / 2.91 ( 1960) Misc. bond : bond 0.10209 / 5.12 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 166 time to evaluate : 0.258 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 167 average time/residue: 0.7116 time to fit residues: 125.5117 Evaluate side-chains 113 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 9.9990 chunk 106 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 39 HIS G 73 ASN H 92 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.077202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.054636 restraints weight = 35756.004| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 1.56 r_work: 0.2832 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9098 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 13675 Z= 0.163 Angle : 0.713 9.152 19721 Z= 0.404 Chirality : 0.051 0.363 2229 Planarity : 0.005 0.043 1477 Dihedral : 32.083 167.549 4163 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.26 % Allowed : 22.30 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.29), residues: 831 helix: 2.19 (0.22), residues: 561 sheet: 0.59 (1.85), residues: 10 loop : -1.02 (0.35), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 83 TYR 0.021 0.001 TYR K 61 PHE 0.012 0.002 PHE K 5 TRP 0.007 0.002 TRP K 21 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.16 (13673) covalent geometry : angle 0.71292 / 0.40 (19721) hydrogen bonds : bond 0.05244 / 3.57 ( 785) hydrogen bonds : angle 3.06413 / 2.28 ( 1960) Misc. bond : bond 0.00385 / 0.20 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.201 Fit side-chains revert: symmetry clash REVERT: E 97 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8329 (mp0) REVERT: K 87 ASN cc_start: 0.8084 (t0) cc_final: 0.7798 (t0) outliers start: 9 outliers final: 4 residues processed: 123 average time/residue: 0.7140 time to fit residues: 93.1116 Evaluate side-chains 117 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 112 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 58 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 47 optimal weight: 3.9990 chunk 78 optimal weight: 8.9990 chunk 105 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 chunk 97 optimal weight: 10.0000 chunk 104 optimal weight: 9.9990 chunk 54 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 100 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 46 HIS ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.074373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.051636 restraints weight = 35937.806| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 1.57 r_work: 0.2751 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9172 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13675 Z= 0.198 Angle : 0.693 10.998 19721 Z= 0.391 Chirality : 0.050 0.372 2229 Planarity : 0.005 0.057 1477 Dihedral : 31.708 171.445 4163 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.96 % Allowed : 20.76 % Favored : 77.28 % 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: 2.08 (0.29), residues: 831 helix: 2.39 (0.22), residues: 563 sheet: -1.27 (1.01), residues: 21 loop : -0.82 (0.35), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 74 TYR 0.020 0.002 TYR K 61 PHE 0.009 0.002 PHE E 104 TRP 0.002 0.001 TRP K 21 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.20 (13673) covalent geometry : angle 0.69281 / 0.39 (19721) hydrogen bonds : bond 0.05400 / 3.70 ( 785) hydrogen bonds : angle 2.94186 / 2.19 ( 1960) Misc. bond : bond 0.00668 / 0.34 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: D 68 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8614 (tm-30) REVERT: E 97 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8393 (mp0) REVERT: F 20 LYS cc_start: 0.7300 (OUTLIER) cc_final: 0.6745 (mmmt) REVERT: K 45 PHE cc_start: 0.8018 (m-80) cc_final: 0.7695 (m-10) REVERT: K 63 GLU cc_start: 0.8925 (tp30) cc_final: 0.8687 (tm-30) REVERT: K 74 ARG cc_start: 0.8143 (mmt90) cc_final: 0.7806 (mmt90) outliers start: 14 outliers final: 4 residues processed: 125 average time/residue: 0.6827 time to fit residues: 90.4806 Evaluate side-chains 118 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 112 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 20 LYS Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 58 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.0670 chunk 107 optimal weight: 10.0000 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 44 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.074709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.052053 restraints weight = 36084.380| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 1.58 r_work: 0.2767 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9159 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13675 Z= 0.153 Angle : 0.657 12.357 19721 Z= 0.372 Chirality : 0.047 0.372 2229 Planarity : 0.004 0.042 1477 Dihedral : 31.588 172.351 4163 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.68 % Allowed : 21.60 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.29), residues: 831 helix: 2.54 (0.22), residues: 563 sheet: -1.63 (0.93), residues: 21 loop : -0.67 (0.35), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 83 TYR 0.011 0.001 TYR K 61 PHE 0.007 0.001 PHE A 67 TRP 0.004 0.001 TRP K 82 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.15 (13673) covalent geometry : angle 0.65725 / 0.37 (19721) hydrogen bonds : bond 0.04689 / 3.20 ( 785) hydrogen bonds : angle 2.82814 / 2.11 ( 1960) Misc. bond : bond 0.00059 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: C 90 ASP cc_start: 0.8940 (t0) cc_final: 0.8722 (t70) REVERT: D 54 LYS cc_start: 0.8889 (mmmm) cc_final: 0.8676 (mmtm) REVERT: D 68 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8613 (tm-30) REVERT: E 120 MET cc_start: 0.9251 (mtt) cc_final: 0.8990 (mtt) REVERT: K 45 PHE cc_start: 0.7896 (m-80) cc_final: 0.7647 (m-10) REVERT: K 53 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8959 (tt) REVERT: K 63 GLU cc_start: 0.8935 (tp30) cc_final: 0.8705 (tm-30) outliers start: 12 outliers final: 5 residues processed: 120 average time/residue: 0.7545 time to fit residues: 96.1688 Evaluate side-chains 121 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 115 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 53 LEU Chi-restraints excluded: chain K residue 58 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 28 optimal weight: 0.4980 chunk 5 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 87 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 chunk 82 optimal weight: 9.9990 chunk 23 optimal weight: 0.2980 chunk 40 optimal weight: 3.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 44 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.073778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.051101 restraints weight = 35997.999| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 1.56 r_work: 0.2740 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9189 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13675 Z= 0.179 Angle : 0.662 9.450 19721 Z= 0.375 Chirality : 0.049 0.470 2229 Planarity : 0.004 0.041 1477 Dihedral : 31.504 174.160 4163 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.96 % Allowed : 21.74 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.34 (0.29), residues: 831 helix: 2.60 (0.22), residues: 558 sheet: -2.35 (1.00), residues: 18 loop : -0.61 (0.34), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 83 TYR 0.013 0.001 TYR K 61 PHE 0.008 0.001 PHE A 67 TRP 0.004 0.001 TRP K 82 HIS 0.002 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.18 (13673) covalent geometry : angle 0.66155 / 0.37 (19721) hydrogen bonds : bond 0.05028 / 3.42 ( 785) hydrogen bonds : angle 2.84666 / 2.12 ( 1960) Misc. bond : bond 0.00049 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: C 90 ASP cc_start: 0.8960 (t70) cc_final: 0.8713 (t70) REVERT: D 68 GLU cc_start: 0.8898 (mm-30) cc_final: 0.8616 (tm-30) REVERT: E 97 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8560 (mp0) REVERT: E 120 MET cc_start: 0.9244 (mtt) cc_final: 0.8991 (mtt) REVERT: F 20 LYS cc_start: 0.7288 (OUTLIER) cc_final: 0.6696 (mmmt) REVERT: H 90 GLU cc_start: 0.9222 (OUTLIER) cc_final: 0.8171 (mp0) REVERT: K 1 MET cc_start: 0.2101 (ptp) cc_final: 0.0897 (ptt) REVERT: K 9 ASP cc_start: 0.6884 (t0) cc_final: 0.6683 (t0) REVERT: K 63 GLU cc_start: 0.8932 (tp30) cc_final: 0.8701 (tm-30) outliers start: 14 outliers final: 6 residues processed: 124 average time/residue: 0.7196 time to fit residues: 94.6936 Evaluate side-chains 123 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 20 LYS Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 58 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 62 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 59.8711 > 50:) chunk 64 optimal weight: 0.2980 chunk 107 optimal weight: 9.9990 chunk 1 optimal weight: 0.9980 chunk 45 optimal weight: 0.0770 chunk 86 optimal weight: 6.9990 chunk 78 optimal weight: 8.9990 chunk 63 optimal weight: 0.9980 chunk 4 optimal weight: 0.0980 chunk 93 optimal weight: 0.0980 chunk 10 optimal weight: 0.9990 overall best weight: 0.3138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN D 44 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.074462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.051934 restraints weight = 35487.960| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 1.56 r_work: 0.2767 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9166 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 13675 Z= 0.128 Angle : 0.638 9.446 19721 Z= 0.365 Chirality : 0.047 0.365 2229 Planarity : 0.004 0.069 1477 Dihedral : 31.462 174.409 4163 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.40 % Allowed : 22.44 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.45 (0.29), residues: 831 helix: 2.69 (0.22), residues: 558 sheet: -1.62 (1.36), residues: 12 loop : -0.66 (0.34), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 83 TYR 0.010 0.001 TYR K 61 PHE 0.008 0.001 PHE A 67 TRP 0.004 0.001 TRP K 82 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.13 (13673) covalent geometry : angle 0.63816 / 0.36 (19721) hydrogen bonds : bond 0.04570 / 3.10 ( 785) hydrogen bonds : angle 2.80946 / 2.09 ( 1960) Misc. bond : bond 0.00009 / 0.00 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: D 68 GLU cc_start: 0.8882 (mm-30) cc_final: 0.8612 (tm-30) REVERT: E 120 MET cc_start: 0.9227 (mtt) cc_final: 0.8991 (mtt) REVERT: F 20 LYS cc_start: 0.7307 (OUTLIER) cc_final: 0.6741 (mmmt) REVERT: G 92 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8537 (mt-10) REVERT: H 90 GLU cc_start: 0.9206 (OUTLIER) cc_final: 0.8155 (mp0) REVERT: K 1 MET cc_start: 0.2079 (ptp) cc_final: 0.1042 (ptt) REVERT: K 63 GLU cc_start: 0.8943 (tp30) cc_final: 0.8733 (tm-30) REVERT: K 87 ASN cc_start: 0.8038 (t0) cc_final: 0.7802 (t0) outliers start: 10 outliers final: 7 residues processed: 124 average time/residue: 0.7607 time to fit residues: 99.9395 Evaluate side-chains 126 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain F residue 20 LYS Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 58 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 95 optimal weight: 10.0000 chunk 10 optimal weight: 0.6980 chunk 75 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 15 optimal weight: 0.1980 chunk 18 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 55.1139 > 50:) chunk 49 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 71 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 44 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.074715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.052219 restraints weight = 35916.112| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 1.57 r_work: 0.2775 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9158 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 13675 Z= 0.134 Angle : 0.636 10.850 19721 Z= 0.363 Chirality : 0.045 0.369 2229 Planarity : 0.004 0.040 1477 Dihedral : 31.362 174.769 4163 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.26 % Allowed : 23.00 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.59 (0.29), residues: 831 helix: 2.83 (0.21), residues: 557 sheet: -2.57 (0.81), residues: 20 loop : -0.51 (0.35), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 83 TYR 0.009 0.001 TYR K 61 PHE 0.013 0.001 PHE K 52 TRP 0.004 0.001 TRP K 82 HIS 0.004 0.001 HIS K 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.13 (13673) covalent geometry : angle 0.63640 / 0.36 (19721) hydrogen bonds : bond 0.04416 / 3.00 ( 785) hydrogen bonds : angle 2.72953 / 2.03 ( 1960) Misc. bond : bond 0.00019 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 122 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: D 68 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8617 (tm-30) REVERT: E 120 MET cc_start: 0.9227 (mtt) cc_final: 0.9015 (mtt) REVERT: F 20 LYS cc_start: 0.7294 (OUTLIER) cc_final: 0.6738 (mmmt) REVERT: G 92 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8490 (mt-10) REVERT: H 90 GLU cc_start: 0.9199 (OUTLIER) cc_final: 0.8142 (mp0) REVERT: K 1 MET cc_start: 0.2431 (ptp) cc_final: 0.1343 (ptt) REVERT: K 87 ASN cc_start: 0.8137 (t0) cc_final: 0.7835 (t0) outliers start: 9 outliers final: 6 residues processed: 125 average time/residue: 0.8782 time to fit residues: 116.6459 Evaluate side-chains 125 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 116 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain F residue 20 LYS Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 58 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 11 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 57 optimal weight: 0.5980 chunk 75 optimal weight: 9.9990 chunk 91 optimal weight: 0.9990 chunk 84 optimal weight: 8.9990 chunk 18 optimal weight: 8.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.074508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.052073 restraints weight = 35648.804| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 1.55 r_work: 0.2770 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9163 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13675 Z= 0.144 Angle : 0.633 9.500 19721 Z= 0.361 Chirality : 0.046 0.369 2229 Planarity : 0.004 0.041 1477 Dihedral : 31.320 174.954 4163 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.40 % Allowed : 23.42 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.65 (0.29), residues: 831 helix: 2.85 (0.21), residues: 557 sheet: -2.52 (0.85), residues: 20 loop : -0.45 (0.35), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 83 TYR 0.009 0.001 TYR K 61 PHE 0.007 0.001 PHE A 67 TRP 0.003 0.001 TRP K 82 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.14 (13673) covalent geometry : angle 0.63251 / 0.36 (19721) hydrogen bonds : bond 0.04459 / 3.02 ( 785) hydrogen bonds : angle 2.72041 / 2.03 ( 1960) Misc. bond : bond 0.00021 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: C 90 ASP cc_start: 0.8920 (t0) cc_final: 0.8705 (t70) REVERT: D 68 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8615 (tm-30) REVERT: E 120 MET cc_start: 0.9212 (mtt) cc_final: 0.8995 (mtt) REVERT: F 20 LYS cc_start: 0.7225 (OUTLIER) cc_final: 0.6681 (mmmt) REVERT: G 92 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8464 (mt-10) REVERT: H 90 GLU cc_start: 0.9204 (OUTLIER) cc_final: 0.8140 (mp0) REVERT: K 1 MET cc_start: 0.2510 (ptp) cc_final: 0.1388 (ptt) REVERT: K 63 GLU cc_start: 0.7394 (tm-30) cc_final: 0.5981 (tm-30) REVERT: K 87 ASN cc_start: 0.8189 (t0) cc_final: 0.7889 (t0) outliers start: 10 outliers final: 4 residues processed: 121 average time/residue: 0.9016 time to fit residues: 115.6941 Evaluate side-chains 122 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 115 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain F residue 20 LYS Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 58 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 43 optimal weight: 0.0000 chunk 25 optimal weight: 0.8980 chunk 4 optimal weight: 0.0470 chunk 68 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 chunk 105 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 84 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 overall best weight: 0.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN E 113 HIS ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.074638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.052237 restraints weight = 35832.801| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 1.56 r_work: 0.2779 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9157 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13675 Z= 0.139 Angle : 0.643 11.778 19721 Z= 0.362 Chirality : 0.045 0.369 2229 Planarity : 0.004 0.041 1477 Dihedral : 31.241 175.386 4163 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.54 % Allowed : 23.14 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.72 (0.29), residues: 831 helix: 2.85 (0.21), residues: 563 sheet: -2.39 (0.98), residues: 20 loop : -0.36 (0.36), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 83 TYR 0.010 0.001 TYR K 61 PHE 0.007 0.001 PHE F 61 TRP 0.003 0.001 TRP K 82 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.14 (13673) covalent geometry : angle 0.64264 / 0.36 (19721) hydrogen bonds : bond 0.04361 / 2.95 ( 785) hydrogen bonds : angle 2.66722 / 1.99 ( 1960) Misc. bond : bond 0.00014 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 90 ASP cc_start: 0.8960 (t0) cc_final: 0.8745 (t70) REVERT: D 68 GLU cc_start: 0.8874 (mm-30) cc_final: 0.8604 (tm-30) REVERT: E 120 MET cc_start: 0.9197 (mtt) cc_final: 0.8971 (mtt) REVERT: F 20 LYS cc_start: 0.7229 (OUTLIER) cc_final: 0.6706 (mmmt) REVERT: H 90 GLU cc_start: 0.9184 (OUTLIER) cc_final: 0.8115 (mp0) REVERT: K 1 MET cc_start: 0.2554 (ptp) cc_final: 0.1387 (ptt) REVERT: K 87 ASN cc_start: 0.8174 (t0) cc_final: 0.7916 (t0) outliers start: 11 outliers final: 4 residues processed: 123 average time/residue: 0.8271 time to fit residues: 107.8768 Evaluate side-chains 124 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 118 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain F residue 20 LYS Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 58 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 22 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.074415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.051990 restraints weight = 35919.840| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 1.55 r_work: 0.2770 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9165 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13675 Z= 0.145 Angle : 0.635 11.126 19721 Z= 0.360 Chirality : 0.045 0.369 2229 Planarity : 0.004 0.041 1477 Dihedral : 31.230 175.461 4163 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.98 % Allowed : 24.12 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.76 (0.29), residues: 831 helix: 2.88 (0.21), residues: 562 sheet: -2.37 (1.02), residues: 20 loop : -0.33 (0.36), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 83 TYR 0.010 0.001 TYR K 61 PHE 0.007 0.001 PHE A 67 TRP 0.003 0.001 TRP K 82 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.14 (13673) covalent geometry : angle 0.63498 / 0.36 (19721) hydrogen bonds : bond 0.04475 / 3.03 ( 785) hydrogen bonds : angle 2.67860 / 2.00 ( 1960) Misc. bond : bond 0.00019 / 0.01 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 120 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: D 68 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8598 (tm-30) REVERT: E 120 MET cc_start: 0.9186 (mtt) cc_final: 0.8957 (mtt) REVERT: F 20 LYS cc_start: 0.7314 (OUTLIER) cc_final: 0.6764 (mmmt) REVERT: H 90 GLU cc_start: 0.9187 (OUTLIER) cc_final: 0.8119 (mp0) REVERT: K 1 MET cc_start: 0.2353 (ptp) cc_final: 0.1241 (ptt) REVERT: K 87 ASN cc_start: 0.8219 (t0) cc_final: 0.7990 (t0) outliers start: 7 outliers final: 4 residues processed: 123 average time/residue: 0.8476 time to fit residues: 110.7527 Evaluate side-chains 123 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 117 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain F residue 20 LYS Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 58 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 69 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 70 optimal weight: 0.4980 chunk 65 optimal weight: 1.9990 chunk 105 optimal weight: 9.9990 chunk 101 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 75 optimal weight: 9.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 81 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.074484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.052108 restraints weight = 35746.601| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 1.55 r_work: 0.2775 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9160 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13675 Z= 0.141 Angle : 0.637 11.052 19721 Z= 0.361 Chirality : 0.045 0.368 2229 Planarity : 0.004 0.048 1477 Dihedral : 31.213 175.490 4163 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.98 % Allowed : 24.12 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.79 (0.29), residues: 831 helix: 2.90 (0.21), residues: 562 sheet: -2.46 (1.00), residues: 20 loop : -0.29 (0.36), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG C 29 TYR 0.011 0.001 TYR K 61 PHE 0.007 0.001 PHE F 61 TRP 0.003 0.001 TRP K 82 HIS 0.002 0.000 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.14 (13673) covalent geometry : angle 0.63741 / 0.36 (19721) hydrogen bonds : bond 0.04385 / 2.97 ( 785) hydrogen bonds : angle 2.65837 / 1.98 ( 1960) Misc. bond : bond 0.00015 / 0.01 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4694.38 seconds wall clock time: 80 minutes 24.46 seconds (4824.46 seconds total)