Starting phenix.real_space_refine on Fri Jul 3 06:18:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8peo_17633/07_2026/8peo_17633.cif Found real_map, /net/cci-nas-00/data/ceres_data/8peo_17633/07_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_17633/07_2026/8peo_17633.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8peo_17633/07_2026/8peo_17633.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8peo_17633/07_2026/8peo_17633.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8peo_17633/07_2026/8peo_17633.cif" model { file = "/net/cci-nas-00/data/ceres_data/8peo_17633/07_2026/8peo_17633.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8peo_17633/07_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.80, per 1000 atoms: 0.22 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: 1.07 Conformation dependent library (CDL) restraints added in 364.2 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: 1.72 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: 2.39 Time building geometry restraints manager: 1.41 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: 18266 1.76 - 3.52: 1334 3.52 - 5.28: 99 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: 0.010 Normalize map: mean=0, sd=1: 6.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.680 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.680 ------------------------------------------------------------------------------- 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= 0.558 Angle : 0.901 8.793 19721 Z= 0.749 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 0.90104 / 0.75 (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 : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 167 average time/residue: 0.9333 time to fit residues: 164.5532 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 : 0.345 ------------------------------------------------------------------------------- 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: 10.0000 chunk 106 optimal weight: 9.9990 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 = 0.077206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.054539 restraints weight = 35759.816| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.56 r_work: 0.2834 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9099 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13675 Z= 0.164 Angle : 0.705 9.786 19721 Z= 0.401 Chirality : 0.049 0.337 2229 Planarity : 0.005 0.043 1477 Dihedral : 32.159 166.113 4163 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.40 % Allowed : 21.32 % 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: 1.84 (0.29), residues: 831 helix: 2.21 (0.22), residues: 561 sheet: 0.67 (1.86), residues: 10 loop : -1.05 (0.35), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 83 TYR 0.022 0.001 TYR K 61 PHE 0.012 0.002 PHE K 5 TRP 0.007 0.002 TRP K 21 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.16 (13673) covalent geometry : angle 0.70487 / 0.40 (19721) hydrogen bonds : bond 0.05126 / 3.49 ( 785) hydrogen bonds : angle 3.06104 / 2.28 ( 1960) Misc. bond : bond 0.01222 / 0.62 ( 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: 10 poor density : 117 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: E 97 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8323 (mp0) REVERT: K 87 ASN cc_start: 0.8063 (t0) cc_final: 0.7795 (t0) outliers start: 10 outliers final: 4 residues processed: 123 average time/residue: 0.8489 time to fit residues: 110.7792 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 : 0.348 ------------------------------------------------------------------------------- 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: 10.0000 chunk 53 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 104 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 100 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 46 HIS G 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.073223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.050404 restraints weight = 35865.968| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 1.58 r_work: 0.2717 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9201 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 13675 Z= 0.234 Angle : 0.712 11.153 19721 Z= 0.401 Chirality : 0.051 0.334 2229 Planarity : 0.005 0.040 1477 Dihedral : 31.850 169.829 4163 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.10 % Allowed : 20.34 % Favored : 77.56 % 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: 1.92 (0.29), residues: 831 helix: 2.28 (0.22), residues: 561 sheet: -1.75 (1.00), residues: 23 loop : -0.83 (0.35), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 83 TYR 0.018 0.002 TYR K 61 PHE 0.011 0.002 PHE E 104 TRP 0.003 0.001 TRP K 21 HIS 0.004 0.001 HIS F 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.23 (13673) covalent geometry : angle 0.71229 / 0.40 (19721) hydrogen bonds : bond 0.06047 / 4.13 ( 785) hydrogen bonds : angle 3.01498 / 2.25 ( 1960) Misc. bond : bond 0.00663 / 0.35 ( 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 132 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: C 90 ASP cc_start: 0.9064 (t0) cc_final: 0.8859 (t70) REVERT: D 68 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8618 (tm-30) REVERT: E 97 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8379 (mp0) REVERT: E 120 MET cc_start: 0.9251 (OUTLIER) cc_final: 0.8944 (mtt) REVERT: F 20 LYS cc_start: 0.7267 (OUTLIER) cc_final: 0.6676 (mmmt) REVERT: K 45 PHE cc_start: 0.8025 (m-80) cc_final: 0.7758 (m-10) REVERT: K 63 GLU cc_start: 0.8871 (tp30) cc_final: 0.8647 (tm-30) REVERT: K 74 ARG cc_start: 0.7710 (mmt90) cc_final: 0.7381 (mmt90) outliers start: 15 outliers final: 8 residues processed: 125 average time/residue: 0.8696 time to fit residues: 115.1361 Evaluate side-chains 123 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 20 LYS Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 95 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 Chi-restraints excluded: chain K residue 84 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.0970 chunk 107 optimal weight: 10.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.073718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.051060 restraints weight = 35994.870| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 1.57 r_work: 0.2739 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9188 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13675 Z= 0.170 Angle : 0.661 11.563 19721 Z= 0.375 Chirality : 0.048 0.338 2229 Planarity : 0.004 0.045 1477 Dihedral : 31.745 170.484 4163 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.96 % Allowed : 21.04 % Favored : 77.00 % 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: 2.15 (0.29), residues: 831 helix: 2.43 (0.22), residues: 563 sheet: -1.52 (1.47), residues: 12 loop : -0.78 (0.34), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 83 TYR 0.009 0.001 TYR F 51 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 0.00327 / 0.17 (13673) covalent geometry : angle 0.66127 / 0.38 (19721) hydrogen bonds : bond 0.04983 / 3.40 ( 785) hydrogen bonds : angle 2.89550 / 2.17 ( 1960) Misc. bond : bond 0.00054 / 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 130 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 90 ASP cc_start: 0.9008 (t0) cc_final: 0.8804 (t0) REVERT: D 54 LYS cc_start: 0.8920 (mmmm) cc_final: 0.8718 (mmtm) REVERT: D 68 GLU cc_start: 0.8914 (mm-30) cc_final: 0.8619 (tm-30) REVERT: F 20 LYS cc_start: 0.7279 (OUTLIER) cc_final: 0.6697 (mmmt) REVERT: K 45 PHE cc_start: 0.7903 (m-80) cc_final: 0.7680 (m-10) REVERT: K 53 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.9035 (tt) REVERT: K 63 GLU cc_start: 0.8938 (tp30) cc_final: 0.8703 (tm-30) outliers start: 14 outliers final: 5 residues processed: 121 average time/residue: 0.8908 time to fit residues: 114.1836 Evaluate side-chains 121 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 114 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 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: 3.9990 chunk 5 optimal weight: 0.8980 chunk 88 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 76 optimal weight: 10.0000 chunk 87 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 82 optimal weight: 9.9990 chunk 23 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN D 44 GLN 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 = 0.074382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.051818 restraints weight = 36043.294| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 1.57 r_work: 0.2764 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9167 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13675 Z= 0.144 Angle : 0.623 8.798 19721 Z= 0.362 Chirality : 0.047 0.464 2229 Planarity : 0.004 0.041 1477 Dihedral : 31.576 172.677 4163 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.82 % Allowed : 21.74 % 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: 2.41 (0.29), residues: 831 helix: 2.66 (0.22), residues: 558 sheet: -1.69 (1.35), residues: 12 loop : -0.67 (0.34), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 83 TYR 0.008 0.001 TYR F 51 PHE 0.009 0.001 PHE K 52 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 0.00261 / 0.14 (13673) covalent geometry : angle 0.62320 / 0.36 (19721) hydrogen bonds : bond 0.04572 / 3.11 ( 785) hydrogen bonds : angle 2.78849 / 2.08 ( 1960) Misc. bond : bond 0.00051 / 0.03 ( 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 132 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: D 68 GLU cc_start: 0.8885 (mm-30) cc_final: 0.8605 (tm-30) REVERT: E 120 MET cc_start: 0.9216 (mtt) cc_final: 0.8991 (mtt) REVERT: K 57 ASP cc_start: 0.5661 (OUTLIER) cc_final: 0.5324 (p0) REVERT: K 63 GLU cc_start: 0.8908 (tp30) cc_final: 0.8703 (tm-30) outliers start: 13 outliers final: 5 residues processed: 125 average time/residue: 0.8513 time to fit residues: 112.8983 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 : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 91 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 57 ASP 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 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 107 optimal weight: 9.9990 chunk 1 optimal weight: 0.9990 chunk 45 optimal weight: 0.0370 chunk 86 optimal weight: 7.9990 chunk 78 optimal weight: 8.9990 chunk 63 optimal weight: 0.0980 chunk 4 optimal weight: 0.0040 chunk 93 optimal weight: 0.0570 chunk 10 optimal weight: 0.6980 overall best weight: 0.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 44 GLN E 113 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.075294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.052884 restraints weight = 35705.092| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.57 r_work: 0.2794 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9142 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13675 Z= 0.125 Angle : 0.610 8.796 19721 Z= 0.356 Chirality : 0.045 0.337 2229 Planarity : 0.004 0.041 1477 Dihedral : 31.488 173.392 4163 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.40 % Allowed : 22.30 % 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: 2.58 (0.29), residues: 831 helix: 2.76 (0.22), residues: 562 sheet: -2.04 (1.04), residues: 16 loop : -0.50 (0.35), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 3 TYR 0.006 0.001 TYR F 51 PHE 0.007 0.001 PHE A 67 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 0.00196 / 0.13 (13673) covalent geometry : angle 0.61021 / 0.36 (19721) hydrogen bonds : bond 0.04243 / 2.88 ( 785) hydrogen bonds : angle 2.73201 / 2.04 ( 1960) Misc. bond : bond 0.00013 / 0.01 ( 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 136 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: C 90 ASP cc_start: 0.8879 (t0) cc_final: 0.8647 (t70) REVERT: D 30 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.7970 (ptp-170) REVERT: D 68 GLU cc_start: 0.8857 (mm-30) cc_final: 0.8591 (tm-30) REVERT: E 120 MET cc_start: 0.9218 (mtt) cc_final: 0.9005 (mtt) REVERT: F 20 LYS cc_start: 0.7298 (OUTLIER) cc_final: 0.6763 (mmmt) REVERT: G 92 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.8551 (mt-10) REVERT: H 90 GLU cc_start: 0.9147 (OUTLIER) cc_final: 0.8276 (mp0) REVERT: K 1 MET cc_start: 0.2306 (ptt) cc_final: 0.1595 (ttp) REVERT: K 83 GLU cc_start: 0.8261 (pt0) cc_final: 0.7987 (pt0) REVERT: K 87 ASN cc_start: 0.7976 (t0) cc_final: 0.7759 (t0) outliers start: 10 outliers final: 3 residues processed: 131 average time/residue: 0.7318 time to fit residues: 101.4119 Evaluate side-chains 123 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 116 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 30 ARG 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 K residue 25 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 95 optimal weight: 9.9990 chunk 10 optimal weight: 0.5980 chunk 75 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 49 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 44 GLN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.074059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.051532 restraints weight = 35870.517| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 1.56 r_work: 0.2753 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9180 moved from start: 0.2692 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= 0.168 Angle : 0.630 8.867 19721 Z= 0.363 Chirality : 0.046 0.339 2229 Planarity : 0.004 0.041 1477 Dihedral : 31.493 173.827 4163 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.26 % Allowed : 22.72 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.54 (0.29), residues: 831 helix: 2.75 (0.21), residues: 562 sheet: -2.65 (0.99), residues: 18 loop : -0.54 (0.35), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 23 TYR 0.008 0.001 TYR F 51 PHE 0.007 0.001 PHE A 67 TRP 0.003 0.001 TRP K 82 HIS 0.002 0.001 HIS K 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.17 (13673) covalent geometry : angle 0.63001 / 0.36 (19721) hydrogen bonds : bond 0.04690 / 3.18 ( 785) hydrogen bonds : angle 2.75908 / 2.06 ( 1960) Misc. bond : bond 0.00034 / 0.02 ( 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 127 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: C 90 ASP cc_start: 0.8934 (t0) cc_final: 0.8695 (t70) REVERT: D 68 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8629 (tm-30) REVERT: E 120 MET cc_start: 0.9233 (mtt) cc_final: 0.9002 (mtt) REVERT: F 20 LYS cc_start: 0.7244 (OUTLIER) cc_final: 0.6672 (mmmt) REVERT: H 90 GLU cc_start: 0.9181 (OUTLIER) cc_final: 0.8309 (mp0) REVERT: K 1 MET cc_start: 0.2577 (ptt) cc_final: 0.2101 (ptt) REVERT: K 83 GLU cc_start: 0.8207 (pt0) cc_final: 0.7940 (pt0) REVERT: K 87 ASN cc_start: 0.8071 (t0) cc_final: 0.7774 (t0) outliers start: 9 outliers final: 3 residues processed: 121 average time/residue: 0.8597 time to fit residues: 110.1098 Evaluate side-chains 120 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 115 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 11 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 75 optimal weight: 9.9990 chunk 91 optimal weight: 0.0040 chunk 84 optimal weight: 8.9990 chunk 18 optimal weight: 9.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.074202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.051731 restraints weight = 35688.165| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 1.56 r_work: 0.2761 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9170 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13675 Z= 0.148 Angle : 0.631 10.853 19721 Z= 0.360 Chirality : 0.045 0.336 2229 Planarity : 0.004 0.041 1477 Dihedral : 31.469 174.030 4163 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.98 % Allowed : 23.28 % 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: 2.57 (0.29), residues: 831 helix: 2.77 (0.21), residues: 562 sheet: -2.73 (0.92), residues: 18 loop : -0.50 (0.35), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 83 TYR 0.008 0.001 TYR F 51 PHE 0.008 0.001 PHE K 52 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 0.00275 / 0.15 (13673) covalent geometry : angle 0.63066 / 0.36 (19721) hydrogen bonds : bond 0.04552 / 3.09 ( 785) hydrogen bonds : angle 2.74911 / 2.05 ( 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 126 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 119 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: D 68 GLU cc_start: 0.8881 (mm-30) cc_final: 0.8609 (tm-30) REVERT: E 120 MET cc_start: 0.9235 (mtt) cc_final: 0.8999 (mtt) REVERT: F 20 LYS cc_start: 0.7264 (OUTLIER) cc_final: 0.6708 (mmmt) REVERT: G 92 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8498 (mt-10) REVERT: H 90 GLU cc_start: 0.9172 (OUTLIER) cc_final: 0.8285 (mp0) REVERT: K 1 MET cc_start: 0.2880 (ptt) cc_final: 0.2406 (ptt) REVERT: K 83 GLU cc_start: 0.8224 (pt0) cc_final: 0.8016 (pt0) REVERT: K 87 ASN cc_start: 0.8139 (t0) cc_final: 0.7836 (t0) outliers start: 7 outliers final: 3 residues processed: 122 average time/residue: 0.7757 time to fit residues: 100.3494 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 : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 25 optimal weight: 0.9980 chunk 4 optimal weight: 0.0570 chunk 68 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 105 optimal weight: 10.0000 chunk 59 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 84 optimal weight: 8.9990 chunk 9 optimal weight: 6.9990 overall best weight: 1.1700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.073461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.050947 restraints weight = 35823.282| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 1.56 r_work: 0.2737 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9190 moved from start: 0.2969 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= 0.166 Angle : 0.648 10.008 19721 Z= 0.367 Chirality : 0.046 0.334 2229 Planarity : 0.004 0.040 1477 Dihedral : 31.434 174.525 4163 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.12 % Allowed : 23.56 % 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: 2.57 (0.29), residues: 831 helix: 2.76 (0.21), residues: 562 sheet: -2.41 (0.96), residues: 20 loop : -0.46 (0.35), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 83 TYR 0.009 0.001 TYR H 39 PHE 0.007 0.001 PHE A 67 TRP 0.002 0.001 TRP K 21 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.17 (13673) covalent geometry : angle 0.64751 / 0.37 (19721) hydrogen bonds : bond 0.04865 / 3.29 ( 785) hydrogen bonds : angle 2.75054 / 2.06 ( 1960) Misc. bond : bond 0.00022 / 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 128 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 120 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: D 68 GLU cc_start: 0.8874 (mm-30) cc_final: 0.8610 (tm-30) REVERT: E 120 MET cc_start: 0.9228 (mtt) cc_final: 0.9001 (mtt) REVERT: F 20 LYS cc_start: 0.7291 (OUTLIER) cc_final: 0.6745 (mmmt) REVERT: K 1 MET cc_start: 0.3244 (ptt) cc_final: 0.2773 (ptt) REVERT: K 83 GLU cc_start: 0.8192 (pt0) cc_final: 0.7986 (pt0) REVERT: K 87 ASN cc_start: 0.8170 (t0) cc_final: 0.7915 (t0) outliers start: 8 outliers final: 4 residues processed: 124 average time/residue: 0.7311 time to fit residues: 96.2690 Evaluate side-chains 122 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 117 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 20 LYS 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 58 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 22 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 28 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.072725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.049847 restraints weight = 35985.549| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 1.57 r_work: 0.2691 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2575 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9213 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13675 Z= 0.192 Angle : 0.667 10.725 19721 Z= 0.374 Chirality : 0.047 0.333 2229 Planarity : 0.004 0.040 1477 Dihedral : 31.452 174.272 4163 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.12 % Allowed : 23.56 % 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: 2.48 (0.29), residues: 831 helix: 2.67 (0.21), residues: 562 sheet: -2.44 (1.00), residues: 20 loop : -0.45 (0.35), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 83 TYR 0.011 0.001 TYR K 61 PHE 0.007 0.001 PHE A 104 TRP 0.002 0.001 TRP K 82 HIS 0.002 0.001 HIS K 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.19 (13673) covalent geometry : angle 0.66687 / 0.37 (19721) hydrogen bonds : bond 0.05131 / 3.48 ( 785) hydrogen bonds : angle 2.80366 / 2.10 ( 1960) Misc. bond : bond 0.00028 / 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 123 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: D 68 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8603 (tm-30) REVERT: E 120 MET cc_start: 0.9242 (mtt) cc_final: 0.9017 (mtt) REVERT: F 20 LYS cc_start: 0.7280 (OUTLIER) cc_final: 0.6680 (mmmt) REVERT: K 1 MET cc_start: 0.3078 (ptt) cc_final: 0.2591 (ptt) REVERT: K 83 GLU cc_start: 0.8243 (pt0) cc_final: 0.8023 (pt0) REVERT: K 87 ASN cc_start: 0.8223 (t0) cc_final: 0.8013 (t0) outliers start: 8 outliers final: 5 residues processed: 120 average time/residue: 0.7549 time to fit residues: 96.1628 Evaluate side-chains 120 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 114 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 20 LYS Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 119 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 69 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 105 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 75 optimal weight: 9.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 104 GLN K 64 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.073115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.050223 restraints weight = 35931.597| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 1.58 r_work: 0.2705 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2590 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9198 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13675 Z= 0.152 Angle : 0.649 11.505 19721 Z= 0.367 Chirality : 0.046 0.330 2229 Planarity : 0.004 0.056 1477 Dihedral : 31.435 174.389 4163 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.12 % Allowed : 23.56 % 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: 2.53 (0.29), residues: 831 helix: 2.69 (0.21), residues: 562 sheet: -2.49 (1.00), residues: 20 loop : -0.40 (0.36), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 83 TYR 0.009 0.001 TYR F 51 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 0.00293 / 0.15 (13673) covalent geometry : angle 0.64869 / 0.37 (19721) hydrogen bonds : bond 0.04863 / 3.29 ( 785) hydrogen bonds : angle 2.77157 / 2.07 ( 1960) Misc. bond : bond 0.00021 / 0.01 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4699.75 seconds wall clock time: 80 minutes 35.56 seconds (4835.56 seconds total)