Starting phenix.real_space_refine on Thu Aug 6 08:19:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gmk_51449/08_2026/9gmk_51449.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gmk_51449/08_2026/9gmk_51449.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9gmk_51449/08_2026/9gmk_51449.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gmk_51449/08_2026/9gmk_51449.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gmk_51449/08_2026/9gmk_51449.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gmk_51449/08_2026/9gmk_51449.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 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 296 5.49 5 S 29 5.16 5 C 8255 2.51 5 N 2752 2.21 5 O 3311 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 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: 14643 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 801 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "D" Number of atoms: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 717 Classifications: {'peptide': 92} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 89} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 806 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 724 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "K" Number of atoms: 2662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2662 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 319} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 3014 Classifications: {'DNA': 148} Link IDs: {'rna3p': 147} Chain: "M" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 3054 Classifications: {'DNA': 148} Link IDs: {'rna3p': 147} Time building chain proxies: 2.76, per 1000 atoms: 0.19 Number of scatterers: 14643 At special positions: 0 Unit cell: (98.01, 142.659, 124.146, 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 29 16.00 P 296 15.00 O 3311 8.00 N 2752 7.00 C 8255 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 451.2 milliseconds 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2020 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 3 sheets defined 64.8% alpha, 2.2% beta 136 base pairs and 251 stacking pairs defined. Time for finding SS restraints: 2.19 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.794A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.588A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 50 through 76 removed outlier: 3.844A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.860A 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 37 through 49 Processing helix chain 'D' and resid 56 through 84 Processing helix chain 'D' and resid 90 through 102 removed outlier: 4.158A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU D 102 " --> pdb=" O VAL D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 124 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.572A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.786A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY E 132 " --> pdb=" O ARG E 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.545A pdb=" N GLY F 28 " --> pdb=" O ASN F 25 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 25 through 29' Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 50 through 76 removed outlier: 3.955A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.517A 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 27 through 36 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.530A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 98 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 removed outlier: 4.006A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 124 removed outlier: 3.640A pdb=" N ALA H 124 " --> pdb=" O LYS H 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 11 through 38 removed outlier: 3.697A pdb=" N LYS K 38 " --> pdb=" O ARG K 34 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 54 Processing helix chain 'K' and resid 54 through 76 removed outlier: 3.637A pdb=" N VAL K 58 " --> pdb=" O SER K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 99 Processing helix chain 'K' and resid 107 through 114 Processing helix chain 'K' and resid 146 through 158 Processing helix chain 'K' and resid 171 through 176 Processing helix chain 'K' and resid 250 through 261 Processing helix chain 'K' and resid 271 through 277 removed outlier: 3.782A pdb=" N TYR K 277 " --> pdb=" O VAL K 273 " (cutoff:3.500A) Processing helix chain 'K' and resid 301 through 307 removed outlier: 3.683A pdb=" N ASP K 305 " --> pdb=" O THR K 301 " (cutoff:3.500A) Processing helix chain 'K' and resid 314 through 327 Processing helix chain 'K' and resid 338 through 344 removed outlier: 4.510A pdb=" N SER K 342 " --> pdb=" O ASP K 338 " (cutoff:3.500A) Processing helix chain 'K' and resid 350 through 355 removed outlier: 3.877A pdb=" N SER K 354 " --> pdb=" O GLY K 350 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.700A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'K' and resid 183 through 185 removed outlier: 6.318A pdb=" N VAL K 164 " --> pdb=" O SER K 184 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N VAL K 103 " --> pdb=" O LEU K 265 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N LEU K 267 " --> pdb=" O VAL K 103 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N TYR K 105 " --> pdb=" O LEU K 267 " (cutoff:3.500A) removed outlier: 9.974A pdb=" N LEU K 311 " --> pdb=" O LEU K 293 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ILE K 295 " --> pdb=" O LEU K 311 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 192 through 194 498 hydrogen bonds defined for protein. 1482 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 339 hydrogen bonds 670 hydrogen bond angles 0 basepair planarities 136 basepair parallelities 251 stacking parallelities Total time for adding SS restraints: 3.13 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3607 1.34 - 1.46: 4444 1.46 - 1.58: 6815 1.58 - 1.70: 590 1.70 - 1.82: 46 Bond restraints: 15502 Sorted by residual: bond pdb=" C3' DG M 127 " pdb=" C2' DG M 127 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.22e+01 bond pdb=" C3' DG L 53 " pdb=" C2' DG L 53 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.12e+01 bond pdb=" C3' DT M 87 " pdb=" C2' DT M 87 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.10e+01 bond pdb=" C3' DT M 158 " pdb=" C2' DT M 158 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DG L 114 " pdb=" C2' DG L 114 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.99e+00 ... (remaining 15497 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 21577 2.27 - 4.55: 544 4.55 - 6.82: 57 6.82 - 9.09: 16 9.09 - 11.36: 3 Bond angle restraints: 22197 Sorted by residual: angle pdb=" N VAL A 117 " pdb=" CA VAL A 117 " pdb=" C VAL A 117 " ideal model delta sigma weight residual 113.42 107.13 6.29 1.17e+00 7.31e-01 2.89e+01 angle pdb=" C LEU H 101 " pdb=" N LEU H 102 " pdb=" CA LEU H 102 " ideal model delta sigma weight residual 122.31 111.33 10.98 2.34e+00 1.83e-01 2.20e+01 angle pdb=" N VAL E 117 " pdb=" CA VAL E 117 " pdb=" C VAL E 117 " ideal model delta sigma weight residual 113.10 108.74 4.36 9.70e-01 1.06e+00 2.02e+01 angle pdb=" N GLU H 71 " pdb=" CA GLU H 71 " pdb=" CB GLU H 71 " ideal model delta sigma weight residual 110.28 117.22 -6.94 1.55e+00 4.16e-01 2.01e+01 angle pdb=" N3 DT M 37 " pdb=" C4 DT M 37 " pdb=" O4 DT M 37 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.99e+01 ... (remaining 22192 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.88: 7196 34.88 - 69.76: 1422 69.76 - 104.64: 13 104.64 - 139.52: 2 139.52 - 174.40: 3 Dihedral angle restraints: 8636 sinusoidal: 5507 harmonic: 3129 Sorted by residual: dihedral pdb=" C4' DT M 87 " pdb=" C3' DT M 87 " pdb=" O3' DT M 87 " pdb=" P DT M 88 " ideal model delta sinusoidal sigma weight residual -140.00 34.40 -174.40 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DC L 98 " pdb=" C3' DC L 98 " pdb=" O3' DC L 98 " pdb=" P DC L 99 " ideal model delta sinusoidal sigma weight residual -140.00 31.73 -171.73 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DA M 66 " pdb=" C3' DA M 66 " pdb=" O3' DA M 66 " pdb=" P DG M 67 " ideal model delta sinusoidal sigma weight residual 220.00 61.32 158.68 1 3.50e+01 8.16e-04 1.51e+01 ... (remaining 8633 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1753 0.043 - 0.086: 546 0.086 - 0.129: 191 0.129 - 0.172: 17 0.172 - 0.214: 7 Chirality restraints: 2514 Sorted by residual: chirality pdb=" CG LEU K 267 " pdb=" CB LEU K 267 " pdb=" CD1 LEU K 267 " pdb=" CD2 LEU K 267 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA PHE E 104 " pdb=" N PHE E 104 " pdb=" C PHE E 104 " pdb=" CB PHE E 104 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA GLU C 61 " pdb=" N GLU C 61 " pdb=" C GLU C 61 " pdb=" CB GLU C 61 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.86e-01 ... (remaining 2511 not shown) Planarity restraints: 1798 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 93 " 0.012 2.00e-02 2.50e+03 2.51e-02 6.29e+00 pdb=" CD GLN A 93 " -0.043 2.00e-02 2.50e+03 pdb=" OE1 GLN A 93 " 0.016 2.00e-02 2.50e+03 pdb=" NE2 GLN A 93 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 99 " -0.015 2.00e-02 2.50e+03 1.70e-02 5.79e+00 pdb=" CG TYR A 99 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR A 99 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR A 99 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 99 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 99 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR A 99 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 99 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN H 67 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.09e+00 pdb=" C ASN H 67 " 0.039 2.00e-02 2.50e+03 pdb=" O ASN H 67 " -0.015 2.00e-02 2.50e+03 pdb=" N ASP H 68 " -0.013 2.00e-02 2.50e+03 ... (remaining 1795 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 541 2.68 - 3.24: 13992 3.24 - 3.79: 28017 3.79 - 4.35: 35199 4.35 - 4.90: 49173 Nonbonded interactions: 126922 Sorted by model distance: nonbonded pdb=" N2 DG L 26 " pdb=" O2 DC M 172 " model vdw 2.126 2.496 nonbonded pdb=" OD2 ASP B 68 " pdb=" NE2 GLN B 93 " model vdw 2.158 3.120 nonbonded pdb=" O GLY B 94 " pdb=" NZ LYS G 99 " model vdw 2.166 3.120 nonbonded pdb=" N GLN C 24 " pdb=" OE2 GLU C 56 " model vdw 2.205 3.120 nonbonded pdb=" O ASN K 189 " pdb=" OG1 THR K 235 " model vdw 2.210 3.040 ... (remaining 126917 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 40 through 134) } ncs_group { reference = (chain 'B' and resid 25 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 15 through 118) } ncs_group { reference = (chain 'D' and resid 34 through 124) selection = (chain 'H' and resid 34 through 124) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.680 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6434 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 0.055 15502 Z= 0.470 Angle : 0.856 11.363 22197 Z= 0.661 Chirality : 0.047 0.214 2514 Planarity : 0.005 0.053 1798 Dihedral : 26.231 174.403 6616 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 21.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.33 % Allowed : 0.55 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.24), residues: 1061 helix: 0.63 (0.20), residues: 648 sheet: 0.94 (0.84), residues: 42 loop : -0.25 (0.28), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 131 TYR 0.041 0.002 TYR A 99 PHE 0.023 0.003 PHE D 65 TRP 0.021 0.003 TRP K 281 HIS 0.007 0.001 HIS K 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.47 (15502) covalent geometry : angle 0.85647 / 0.66 (22197) hydrogen bonds : bond 0.11633 / 7.70 ( 837) hydrogen bonds : angle 5.20619 / 3.72 ( 2152) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 378 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7763 (tp30) cc_final: 0.6734 (tp30) REVERT: B 22 LEU cc_start: 0.4452 (mt) cc_final: 0.4179 (mt) REVERT: B 27 GLN cc_start: 0.8573 (mp10) cc_final: 0.7835 (mp10) REVERT: B 77 LYS cc_start: 0.9163 (mtpt) cc_final: 0.8472 (tptt) REVERT: B 87 VAL cc_start: 0.8359 (t) cc_final: 0.7902 (t) REVERT: C 25 PHE cc_start: 0.5903 (m-80) cc_final: 0.5307 (m-80) REVERT: C 32 ARG cc_start: 0.7670 (ttm170) cc_final: 0.7150 (ttp80) REVERT: C 38 ASN cc_start: 0.7678 (t0) cc_final: 0.6983 (t0) REVERT: C 39 TYR cc_start: 0.6871 (m-10) cc_final: 0.6664 (m-10) REVERT: C 68 ASN cc_start: 0.9407 (m110) cc_final: 0.9103 (m-40) REVERT: C 102 ILE cc_start: 0.8188 (tp) cc_final: 0.7080 (tp) REVERT: C 107 VAL cc_start: 0.7842 (m) cc_final: 0.7239 (t) REVERT: D 43 LYS cc_start: 0.9050 (mmtt) cc_final: 0.8764 (mtpt) REVERT: D 96 THR cc_start: 0.6681 (p) cc_final: 0.6289 (p) REVERT: D 98 VAL cc_start: 0.6123 (t) cc_final: 0.5640 (t) REVERT: D 99 ARG cc_start: 0.5334 (mtp85) cc_final: 0.4944 (ptp-170) REVERT: E 60 LEU cc_start: 0.7817 (mm) cc_final: 0.7230 (mt) REVERT: E 65 LEU cc_start: 0.7919 (mt) cc_final: 0.7570 (mt) REVERT: E 68 GLN cc_start: 0.7660 (mp-120) cc_final: 0.6762 (tp40) REVERT: E 101 VAL cc_start: 0.5789 (m) cc_final: 0.5548 (p) REVERT: F 31 LYS cc_start: 0.8523 (tttt) cc_final: 0.8229 (tmtt) REVERT: F 34 ILE cc_start: 0.5994 (mt) cc_final: 0.5162 (mp) REVERT: F 45 ARG cc_start: 0.6595 (tpt-90) cc_final: 0.5633 (mmm160) REVERT: F 47 SER cc_start: 0.7966 (t) cc_final: 0.7544 (m) REVERT: F 55 ARG cc_start: 0.7054 (mtt180) cc_final: 0.6743 (mtt-85) REVERT: F 97 LEU cc_start: 0.6918 (tp) cc_final: 0.6291 (tp) REVERT: G 32 ARG cc_start: 0.7723 (ttp80) cc_final: 0.7135 (ttp-170) REVERT: G 38 ASN cc_start: 0.6009 (t0) cc_final: 0.5338 (t0) REVERT: G 57 TYR cc_start: 0.6231 (t80) cc_final: 0.5567 (t80) REVERT: G 107 VAL cc_start: 0.7147 (p) cc_final: 0.6465 (t) REVERT: G 108 LEU cc_start: 0.6522 (mm) cc_final: 0.6282 (mt) REVERT: G 115 LEU cc_start: 0.8014 (mt) cc_final: 0.7793 (tt) REVERT: H 51 ASP cc_start: 0.8663 (p0) cc_final: 0.8440 (p0) REVERT: K 12 LYS cc_start: 0.8654 (mmpt) cc_final: 0.8351 (mmtt) REVERT: K 283 MET cc_start: 0.5233 (mmm) cc_final: 0.4430 (mmm) REVERT: K 319 MET cc_start: 0.8464 (mmm) cc_final: 0.7922 (mmm) outliers start: 3 outliers final: 0 residues processed: 380 average time/residue: 0.1592 time to fit residues: 80.1333 Evaluate side-chains 203 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 40.0000 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 30.0000 chunk 55 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS K 24 GLN ** K 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.123968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.091945 restraints weight = 54482.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.094096 restraints weight = 26752.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.095387 restraints weight = 17477.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.096114 restraints weight = 13721.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.096504 restraints weight = 12092.870| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.145 15502 Z= 0.285 Angle : 0.861 17.854 22197 Z= 0.482 Chirality : 0.051 0.317 2514 Planarity : 0.008 0.105 1798 Dihedral : 30.114 171.321 4471 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 18.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 4.32 % Allowed : 15.95 % Favored : 79.73 % 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: 0.16 (0.25), residues: 1061 helix: 0.39 (0.19), residues: 676 sheet: 0.68 (0.85), residues: 44 loop : -0.31 (0.31), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 35 TYR 0.030 0.003 TYR B 88 PHE 0.035 0.004 PHE E 67 TRP 0.012 0.002 TRP K 251 HIS 0.012 0.003 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00602 / 0.28 (15502) covalent geometry : angle 0.86149 / 0.48 (22197) hydrogen bonds : bond 0.07310 / 4.84 ( 837) hydrogen bonds : angle 4.12993 / 2.98 ( 2152) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 219 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8827 (tp30) cc_final: 0.8334 (tp30) REVERT: A 93 GLN cc_start: 0.8897 (mm-40) cc_final: 0.8677 (mm110) REVERT: B 27 GLN cc_start: 0.8320 (mp10) cc_final: 0.8056 (mp10) REVERT: B 77 LYS cc_start: 0.9198 (mtpt) cc_final: 0.8713 (tptt) REVERT: C 81 ARG cc_start: 0.7271 (tpt170) cc_final: 0.6904 (tpp-160) REVERT: D 108 LYS cc_start: 0.7912 (mttt) cc_final: 0.7294 (mmtt) REVERT: E 53 ARG cc_start: 0.8428 (ptm160) cc_final: 0.8180 (ptp-170) REVERT: E 63 ARG cc_start: 0.7336 (mpt180) cc_final: 0.7075 (mmt180) REVERT: E 125 GLN cc_start: 0.8720 (mt0) cc_final: 0.8400 (mp10) REVERT: F 63 GLU cc_start: 0.7577 (pp20) cc_final: 0.7365 (pp20) REVERT: F 85 ASP cc_start: 0.9046 (m-30) cc_final: 0.8802 (m-30) REVERT: G 38 ASN cc_start: 0.7462 (t0) cc_final: 0.6756 (t0) REVERT: G 51 MET cc_start: 0.8417 (mmp) cc_final: 0.8043 (mmm) REVERT: K 18 ARG cc_start: 0.7937 (pmt-80) cc_final: 0.7612 (tpt90) REVERT: K 23 GLU cc_start: 0.8811 (tp30) cc_final: 0.8556 (tm-30) REVERT: K 47 GLU cc_start: 0.6060 (tm-30) cc_final: 0.4910 (pt0) REVERT: K 150 MET cc_start: 0.5551 (mmp) cc_final: 0.5324 (mmp) REVERT: K 283 MET cc_start: 0.5455 (mmm) cc_final: 0.4673 (mmm) REVERT: K 319 MET cc_start: 0.8563 (mmm) cc_final: 0.7763 (mmt) outliers start: 39 outliers final: 19 residues processed: 243 average time/residue: 0.1236 time to fit residues: 41.6837 Evaluate side-chains 184 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 165 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 24 GLN Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 325 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 3 optimal weight: 0.9990 chunk 80 optimal weight: 30.0000 chunk 28 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 102 optimal weight: 20.0000 chunk 21 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 82 HIS E 68 GLN E 85 GLN E 108 ASN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.125739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.092548 restraints weight = 53549.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.094834 restraints weight = 26054.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.096141 restraints weight = 16957.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.096888 restraints weight = 13328.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.097315 restraints weight = 11760.992| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15502 Z= 0.157 Angle : 0.668 8.908 22197 Z= 0.383 Chirality : 0.043 0.288 2514 Planarity : 0.005 0.074 1798 Dihedral : 30.136 171.111 4471 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.88 % Allowed : 18.94 % Favored : 77.19 % 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: 0.78 (0.25), residues: 1061 helix: 0.93 (0.20), residues: 673 sheet: 1.14 (0.88), residues: 42 loop : -0.22 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 79 TYR 0.029 0.002 TYR B 88 PHE 0.026 0.002 PHE D 65 TRP 0.009 0.001 TRP K 251 HIS 0.009 0.001 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.16 (15502) covalent geometry : angle 0.66758 / 0.38 (22197) hydrogen bonds : bond 0.05370 / 3.61 ( 837) hydrogen bonds : angle 3.62128 / 2.64 ( 2152) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 189 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8713 (tp30) cc_final: 0.8435 (tp30) REVERT: B 77 LYS cc_start: 0.9178 (mtpt) cc_final: 0.8713 (tptt) REVERT: C 25 PHE cc_start: 0.7803 (m-80) cc_final: 0.7369 (m-80) REVERT: D 59 MET cc_start: 0.9009 (tpt) cc_final: 0.8396 (tpt) REVERT: D 108 LYS cc_start: 0.7743 (mttt) cc_final: 0.7118 (mmtt) REVERT: E 50 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7768 (tt0) REVERT: E 63 ARG cc_start: 0.7238 (mpt180) cc_final: 0.6867 (mmt180) REVERT: F 31 LYS cc_start: 0.9053 (tttm) cc_final: 0.8830 (tmtt) REVERT: F 85 ASP cc_start: 0.9091 (m-30) cc_final: 0.8860 (m-30) REVERT: F 88 TYR cc_start: 0.8573 (m-10) cc_final: 0.8095 (m-10) REVERT: G 36 LYS cc_start: 0.8248 (mmtp) cc_final: 0.7954 (mmtm) REVERT: G 84 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.7297 (tm-30) REVERT: K 23 GLU cc_start: 0.8881 (tp30) cc_final: 0.8574 (tm-30) REVERT: K 47 GLU cc_start: 0.6189 (tm-30) cc_final: 0.5160 (pt0) REVERT: K 150 MET cc_start: 0.5310 (mmp) cc_final: 0.5076 (mmp) REVERT: K 283 MET cc_start: 0.5486 (mmm) cc_final: 0.4615 (mmm) REVERT: K 319 MET cc_start: 0.8477 (mmm) cc_final: 0.7685 (mmt) outliers start: 35 outliers final: 13 residues processed: 212 average time/residue: 0.1151 time to fit residues: 34.8181 Evaluate side-chains 180 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 165 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 85 GLN Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 84 GLN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 88 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 82 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 128 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 89 optimal weight: 0.0040 chunk 53 optimal weight: 1.9990 chunk 111 optimal weight: 9.9990 overall best weight: 1.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN E 108 ASN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.122854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.089196 restraints weight = 52888.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.091455 restraints weight = 25236.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.092758 restraints weight = 16311.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.093499 restraints weight = 12837.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.093842 restraints weight = 11268.955| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 15502 Z= 0.179 Angle : 0.674 8.022 22197 Z= 0.382 Chirality : 0.044 0.382 2514 Planarity : 0.005 0.085 1798 Dihedral : 30.167 170.857 4471 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 4.21 % Allowed : 20.49 % Favored : 75.30 % 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: 0.99 (0.25), residues: 1061 helix: 1.09 (0.20), residues: 673 sheet: 1.22 (0.89), residues: 42 loop : -0.12 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 154 TYR 0.034 0.002 TYR H 83 PHE 0.025 0.002 PHE D 65 TRP 0.009 0.001 TRP K 251 HIS 0.008 0.001 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.18 (15502) covalent geometry : angle 0.67385 / 0.38 (22197) hydrogen bonds : bond 0.05383 / 3.61 ( 837) hydrogen bonds : angle 3.56216 / 2.59 ( 2152) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 183 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8794 (tp30) cc_final: 0.8187 (tp30) REVERT: A 90 MET cc_start: 0.8652 (mmm) cc_final: 0.8436 (mmp) REVERT: B 77 LYS cc_start: 0.9202 (mtpt) cc_final: 0.8766 (tptt) REVERT: D 59 MET cc_start: 0.9005 (tpt) cc_final: 0.8433 (tpt) REVERT: D 89 ILE cc_start: 0.7546 (OUTLIER) cc_final: 0.7243 (tt) REVERT: D 108 LYS cc_start: 0.7791 (mttt) cc_final: 0.7171 (mmtt) REVERT: E 63 ARG cc_start: 0.7272 (mpt180) cc_final: 0.7020 (mmt180) REVERT: F 31 LYS cc_start: 0.9128 (tttm) cc_final: 0.8868 (tmtt) REVERT: F 84 MET cc_start: 0.8527 (tpp) cc_final: 0.8315 (tpp) REVERT: F 85 ASP cc_start: 0.9087 (m-30) cc_final: 0.8862 (m-30) REVERT: G 36 LYS cc_start: 0.8484 (mmtp) cc_final: 0.8174 (mmtm) REVERT: H 79 ARG cc_start: 0.8433 (ttm-80) cc_final: 0.7970 (ttm-80) REVERT: K 23 GLU cc_start: 0.8867 (tp30) cc_final: 0.8539 (tm-30) REVERT: K 47 GLU cc_start: 0.6320 (tm-30) cc_final: 0.5331 (pt0) REVERT: K 105 TYR cc_start: 0.7246 (m-80) cc_final: 0.5874 (m-10) REVERT: K 265 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7265 (mm) REVERT: K 283 MET cc_start: 0.5366 (mmm) cc_final: 0.4585 (mmm) REVERT: K 293 LEU cc_start: 0.7212 (OUTLIER) cc_final: 0.6412 (mp) REVERT: K 319 MET cc_start: 0.8398 (mmm) cc_final: 0.7720 (mmt) outliers start: 38 outliers final: 20 residues processed: 204 average time/residue: 0.1140 time to fit residues: 33.7412 Evaluate side-chains 186 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 54 TYR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 85 GLN Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 265 LEU Chi-restraints excluded: chain K residue 293 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 94 optimal weight: 40.0000 chunk 90 optimal weight: 30.0000 chunk 87 optimal weight: 20.0000 chunk 92 optimal weight: 0.0070 chunk 8 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 43 optimal weight: 0.0980 chunk 105 optimal weight: 30.0000 chunk 91 optimal weight: 4.9990 chunk 97 optimal weight: 8.9990 chunk 102 optimal weight: 40.0000 overall best weight: 4.4204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 173 HIS ** 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 = 0.4181 r_free = 0.4181 target = 0.115043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.079582 restraints weight = 53480.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.081642 restraints weight = 26079.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.082858 restraints weight = 17362.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.083559 restraints weight = 13931.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.083861 restraints weight = 12381.369| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.5883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.136 15502 Z= 0.299 Angle : 0.816 18.596 22197 Z= 0.457 Chirality : 0.048 0.295 2514 Planarity : 0.007 0.071 1798 Dihedral : 30.388 169.579 4471 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 19.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 6.76 % Allowed : 21.26 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.25), residues: 1061 helix: 0.70 (0.20), residues: 683 sheet: 0.87 (0.84), residues: 42 loop : -0.32 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 74 TYR 0.055 0.004 TYR H 83 PHE 0.025 0.004 PHE D 65 TRP 0.020 0.003 TRP K 300 HIS 0.009 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00613 / 0.30 (15502) covalent geometry : angle 0.81639 / 0.46 (22197) hydrogen bonds : bond 0.06867 / 4.58 ( 837) hydrogen bonds : angle 3.87814 / 2.82 ( 2152) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 190 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8848 (tp30) cc_final: 0.8233 (tp30) REVERT: B 44 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.8025 (mtpt) REVERT: B 68 ASP cc_start: 0.8720 (m-30) cc_final: 0.8514 (m-30) REVERT: B 77 LYS cc_start: 0.9301 (mtpt) cc_final: 0.8886 (tptt) REVERT: B 88 TYR cc_start: 0.8827 (m-80) cc_final: 0.8383 (m-80) REVERT: C 81 ARG cc_start: 0.7432 (tpt170) cc_final: 0.6911 (tpt170) REVERT: D 106 LEU cc_start: 0.6472 (OUTLIER) cc_final: 0.6161 (tp) REVERT: D 108 LYS cc_start: 0.8116 (mttt) cc_final: 0.7434 (mmtm) REVERT: E 53 ARG cc_start: 0.8516 (ptm160) cc_final: 0.8217 (ptp-170) REVERT: F 63 GLU cc_start: 0.8459 (tp30) cc_final: 0.8111 (tp30) REVERT: F 85 ASP cc_start: 0.9129 (m-30) cc_final: 0.8902 (m-30) REVERT: G 36 LYS cc_start: 0.8861 (mmtp) cc_final: 0.8608 (mmtm) REVERT: G 74 LYS cc_start: 0.8478 (mmtt) cc_final: 0.8001 (tppp) REVERT: G 84 GLN cc_start: 0.9058 (OUTLIER) cc_final: 0.7962 (tm-30) REVERT: K 23 GLU cc_start: 0.8892 (tp30) cc_final: 0.8597 (tm-30) REVERT: K 35 ILE cc_start: 0.7283 (tt) cc_final: 0.6973 (tt) REVERT: K 47 GLU cc_start: 0.6352 (tm-30) cc_final: 0.5457 (pt0) REVERT: K 150 MET cc_start: 0.5387 (mmp) cc_final: 0.5167 (mmp) REVERT: K 190 MET cc_start: 0.0084 (tpt) cc_final: -0.0201 (tpt) REVERT: K 283 MET cc_start: 0.5590 (mmm) cc_final: 0.4814 (mmm) REVERT: K 293 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.6661 (mp) REVERT: K 319 MET cc_start: 0.8445 (mmm) cc_final: 0.7610 (mmt) outliers start: 61 outliers final: 35 residues processed: 228 average time/residue: 0.1318 time to fit residues: 42.2916 Evaluate side-chains 208 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 169 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 54 TYR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 84 GLN Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 239 PHE Chi-restraints excluded: chain K residue 293 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 68 optimal weight: 0.0470 chunk 94 optimal weight: 30.0000 chunk 129 optimal weight: 20.0000 chunk 21 optimal weight: 0.6980 chunk 127 optimal weight: 20.0000 chunk 15 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 overall best weight: 0.9280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN ** K 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.117260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.082039 restraints weight = 52030.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.084220 restraints weight = 24488.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.085498 restraints weight = 15938.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.086095 restraints weight = 12631.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.086542 restraints weight = 11360.133| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.6014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.113 15502 Z= 0.155 Angle : 0.666 7.636 22197 Z= 0.376 Chirality : 0.043 0.278 2514 Planarity : 0.005 0.052 1798 Dihedral : 30.354 170.271 4471 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.99 % Allowed : 24.81 % Favored : 71.21 % 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: 0.97 (0.25), residues: 1061 helix: 1.17 (0.20), residues: 671 sheet: 1.12 (0.88), residues: 42 loop : -0.32 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 79 TYR 0.078 0.002 TYR H 83 PHE 0.026 0.002 PHE D 65 TRP 0.008 0.002 TRP K 251 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.15 (15502) covalent geometry : angle 0.66649 / 0.38 (22197) hydrogen bonds : bond 0.05118 / 3.42 ( 837) hydrogen bonds : angle 3.50155 / 2.55 ( 2152) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 198 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8706 (tp30) cc_final: 0.8102 (tp30) REVERT: B 77 LYS cc_start: 0.9282 (mtpt) cc_final: 0.8854 (tptt) REVERT: D 108 LYS cc_start: 0.8017 (mttt) cc_final: 0.7372 (mmtm) REVERT: E 74 ILE cc_start: 0.9149 (tt) cc_final: 0.8916 (mt) REVERT: E 125 GLN cc_start: 0.8593 (mt0) cc_final: 0.8274 (mp10) REVERT: F 40 ARG cc_start: 0.7511 (ttp80) cc_final: 0.6729 (tpp80) REVERT: G 36 LYS cc_start: 0.8675 (mmtp) cc_final: 0.8399 (mmtm) REVERT: G 71 ARG cc_start: 0.7854 (mtm110) cc_final: 0.7626 (mtm-85) REVERT: G 74 LYS cc_start: 0.8529 (mmtt) cc_final: 0.8007 (tppp) REVERT: G 84 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8670 (tp-100) REVERT: H 62 MET cc_start: 0.9296 (tpp) cc_final: 0.8995 (tpp) REVERT: H 93 GLU cc_start: 0.7786 (mp0) cc_final: 0.7529 (mp0) REVERT: K 11 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.8157 (mmp80) REVERT: K 35 ILE cc_start: 0.7156 (tt) cc_final: 0.6864 (tt) REVERT: K 47 GLU cc_start: 0.6287 (tm-30) cc_final: 0.5416 (pt0) REVERT: K 150 MET cc_start: 0.5261 (mmp) cc_final: 0.5011 (mmp) REVERT: K 265 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7305 (mt) REVERT: K 283 MET cc_start: 0.5617 (mmm) cc_final: 0.4212 (tmm) REVERT: K 293 LEU cc_start: 0.7069 (OUTLIER) cc_final: 0.6298 (mp) REVERT: K 319 MET cc_start: 0.8464 (mmm) cc_final: 0.7744 (mmt) outliers start: 36 outliers final: 20 residues processed: 219 average time/residue: 0.1286 time to fit residues: 40.1451 Evaluate side-chains 197 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 84 GLN Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 239 PHE Chi-restraints excluded: chain K residue 265 LEU Chi-restraints excluded: chain K residue 293 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 112 optimal weight: 20.0000 chunk 48 optimal weight: 2.9990 chunk 110 optimal weight: 20.0000 chunk 94 optimal weight: 30.0000 chunk 66 optimal weight: 3.9990 chunk 64 optimal weight: 0.0970 chunk 19 optimal weight: 2.9990 chunk 102 optimal weight: 40.0000 chunk 86 optimal weight: 6.9990 chunk 107 optimal weight: 30.0000 chunk 42 optimal weight: 4.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.114762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.079471 restraints weight = 53513.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.081528 restraints weight = 25599.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.082717 restraints weight = 16875.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.083389 restraints weight = 13518.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.083698 restraints weight = 12060.466| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.6397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 15502 Z= 0.212 Angle : 0.711 9.198 22197 Z= 0.397 Chirality : 0.045 0.370 2514 Planarity : 0.005 0.055 1798 Dihedral : 30.400 169.808 4471 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.54 % Allowed : 24.81 % Favored : 70.65 % 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: 0.86 (0.25), residues: 1061 helix: 1.05 (0.20), residues: 677 sheet: 1.36 (0.88), residues: 42 loop : -0.34 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 71 TYR 0.101 0.003 TYR H 83 PHE 0.018 0.002 PHE E 67 TRP 0.008 0.001 TRP K 251 HIS 0.007 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.21 (15502) covalent geometry : angle 0.71059 / 0.40 (22197) hydrogen bonds : bond 0.05594 / 3.73 ( 837) hydrogen bonds : angle 3.64375 / 2.67 ( 2152) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 179 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8780 (tp30) cc_final: 0.8147 (tp30) REVERT: A 90 MET cc_start: 0.8820 (mmm) cc_final: 0.8616 (mmp) REVERT: B 77 LYS cc_start: 0.9301 (mtpt) cc_final: 0.8884 (tptt) REVERT: C 51 MET cc_start: 0.8751 (mmp) cc_final: 0.8276 (mmp) REVERT: C 57 TYR cc_start: 0.7447 (t80) cc_final: 0.6594 (t80) REVERT: C 81 ARG cc_start: 0.7529 (tpt170) cc_final: 0.6995 (tpt170) REVERT: D 42 TYR cc_start: 0.8092 (t80) cc_final: 0.7397 (t80) REVERT: D 46 LYS cc_start: 0.8694 (ttpt) cc_final: 0.8192 (pttt) REVERT: D 108 LYS cc_start: 0.8031 (mttt) cc_final: 0.7409 (mmtm) REVERT: E 77 ASP cc_start: 0.8428 (OUTLIER) cc_final: 0.8192 (p0) REVERT: E 125 GLN cc_start: 0.8588 (mt0) cc_final: 0.8308 (mp10) REVERT: F 40 ARG cc_start: 0.7545 (ttp80) cc_final: 0.6731 (tpp80) REVERT: F 46 ILE cc_start: 0.8169 (OUTLIER) cc_final: 0.7619 (tp) REVERT: G 36 LYS cc_start: 0.8879 (mmtp) cc_final: 0.8615 (mmtm) REVERT: G 71 ARG cc_start: 0.8062 (mtm110) cc_final: 0.7744 (mtm-85) REVERT: G 74 LYS cc_start: 0.8648 (mmtt) cc_final: 0.8098 (tppp) REVERT: G 84 GLN cc_start: 0.9054 (OUTLIER) cc_final: 0.8744 (tp-100) REVERT: H 62 MET cc_start: 0.9272 (tpp) cc_final: 0.8956 (tpp) REVERT: K 35 ILE cc_start: 0.7191 (tt) cc_final: 0.6900 (tt) REVERT: K 47 GLU cc_start: 0.6325 (tm-30) cc_final: 0.5430 (pt0) REVERT: K 150 MET cc_start: 0.5186 (mmp) cc_final: 0.4928 (mmp) REVERT: K 283 MET cc_start: 0.5690 (mmm) cc_final: 0.4600 (tpp) REVERT: K 292 LYS cc_start: 0.6082 (mmpt) cc_final: 0.5393 (ptpt) REVERT: K 293 LEU cc_start: 0.6979 (OUTLIER) cc_final: 0.6375 (mp) REVERT: K 319 MET cc_start: 0.8462 (mmm) cc_final: 0.7765 (mmt) outliers start: 41 outliers final: 28 residues processed: 205 average time/residue: 0.1293 time to fit residues: 38.2302 Evaluate side-chains 202 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 170 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 85 GLN Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 84 GLN Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 207 VAL Chi-restraints excluded: chain K residue 239 PHE Chi-restraints excluded: chain K residue 293 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 54 optimal weight: 3.9990 chunk 80 optimal weight: 30.0000 chunk 108 optimal weight: 20.0000 chunk 122 optimal weight: 20.0000 chunk 2 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 116 optimal weight: 30.0000 chunk 17 optimal weight: 10.0000 chunk 84 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 173 HIS ** 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 = 0.4143 r_free = 0.4143 target = 0.112539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.077081 restraints weight = 53616.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.079135 restraints weight = 25339.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.080308 restraints weight = 16669.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.080939 restraints weight = 13367.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.081291 restraints weight = 11996.668| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.6943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 15502 Z= 0.221 Angle : 0.720 9.051 22197 Z= 0.402 Chirality : 0.045 0.280 2514 Planarity : 0.006 0.095 1798 Dihedral : 30.486 169.524 4471 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 4.76 % Allowed : 25.14 % Favored : 70.10 % 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: 0.83 (0.25), residues: 1061 helix: 1.01 (0.20), residues: 680 sheet: 1.28 (0.86), residues: 42 loop : -0.32 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 71 TYR 0.073 0.003 TYR H 83 PHE 0.020 0.003 PHE E 84 TRP 0.007 0.001 TRP K 251 HIS 0.008 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.22 (15502) covalent geometry : angle 0.72035 / 0.40 (22197) hydrogen bonds : bond 0.05579 / 3.72 ( 837) hydrogen bonds : angle 3.68174 / 2.70 ( 2152) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 179 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8755 (tp30) cc_final: 0.8117 (tp30) REVERT: A 90 MET cc_start: 0.8824 (mmm) cc_final: 0.8613 (mmp) REVERT: B 63 GLU cc_start: 0.8377 (pt0) cc_final: 0.7872 (pt0) REVERT: B 77 LYS cc_start: 0.9324 (mtpt) cc_final: 0.8904 (tptt) REVERT: C 57 TYR cc_start: 0.7704 (t80) cc_final: 0.6971 (t80) REVERT: C 81 ARG cc_start: 0.7639 (tpt170) cc_final: 0.7122 (tpt170) REVERT: C 95 LYS cc_start: 0.8825 (tmmt) cc_final: 0.8501 (ttmt) REVERT: D 108 LYS cc_start: 0.8046 (mttt) cc_final: 0.7440 (mmtm) REVERT: E 74 ILE cc_start: 0.9171 (tt) cc_final: 0.8959 (mt) REVERT: E 77 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.8153 (p0) REVERT: E 79 LYS cc_start: 0.8159 (ptmm) cc_final: 0.7948 (pttt) REVERT: E 85 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.7388 (mt0) REVERT: F 40 ARG cc_start: 0.7639 (ttp80) cc_final: 0.6832 (tpp80) REVERT: G 36 LYS cc_start: 0.8899 (mmtp) cc_final: 0.8647 (mmtm) REVERT: G 74 LYS cc_start: 0.8722 (mmtt) cc_final: 0.8177 (tppp) REVERT: G 84 GLN cc_start: 0.9079 (OUTLIER) cc_final: 0.8023 (tm-30) REVERT: H 93 GLU cc_start: 0.8107 (mp0) cc_final: 0.7725 (mp0) REVERT: K 35 ILE cc_start: 0.7246 (tt) cc_final: 0.6960 (tt) REVERT: K 47 GLU cc_start: 0.6400 (tm-30) cc_final: 0.5642 (pt0) REVERT: K 150 MET cc_start: 0.5317 (mmp) cc_final: 0.5068 (mmp) REVERT: K 265 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7261 (mt) REVERT: K 283 MET cc_start: 0.5813 (mmm) cc_final: 0.4727 (tpp) REVERT: K 292 LYS cc_start: 0.6056 (mmpt) cc_final: 0.5383 (ptpt) REVERT: K 293 LEU cc_start: 0.7086 (OUTLIER) cc_final: 0.6394 (mp) REVERT: K 319 MET cc_start: 0.8445 (mmm) cc_final: 0.7766 (mmt) outliers start: 43 outliers final: 30 residues processed: 208 average time/residue: 0.1254 time to fit residues: 37.5719 Evaluate side-chains 207 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 172 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 85 GLN Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 84 GLN Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 207 VAL Chi-restraints excluded: chain K residue 239 PHE Chi-restraints excluded: chain K residue 265 LEU Chi-restraints excluded: chain K residue 293 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 54 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 96 optimal weight: 0.0170 chunk 89 optimal weight: 30.0000 chunk 121 optimal weight: 30.0000 chunk 11 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 127 optimal weight: 20.0000 overall best weight: 1.3422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 173 HIS ** 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 = 0.4162 r_free = 0.4162 target = 0.113819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.078905 restraints weight = 53024.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.080994 restraints weight = 24754.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.082186 restraints weight = 16141.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.082860 restraints weight = 12850.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.083088 restraints weight = 11486.101| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.7034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15502 Z= 0.157 Angle : 0.679 9.605 22197 Z= 0.379 Chirality : 0.043 0.275 2514 Planarity : 0.005 0.046 1798 Dihedral : 30.451 169.806 4471 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.99 % Allowed : 26.80 % Favored : 69.21 % 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: 0.96 (0.25), residues: 1061 helix: 1.07 (0.20), residues: 680 sheet: 1.34 (0.86), residues: 42 loop : -0.19 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 71 TYR 0.086 0.003 TYR H 83 PHE 0.018 0.002 PHE E 67 TRP 0.008 0.001 TRP K 251 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.16 (15502) covalent geometry : angle 0.67850 / 0.38 (22197) hydrogen bonds : bond 0.04989 / 3.35 ( 837) hydrogen bonds : angle 3.54812 / 2.60 ( 2152) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 195 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8697 (tp30) cc_final: 0.8057 (tp30) REVERT: A 90 MET cc_start: 0.8806 (mmm) cc_final: 0.8595 (mmp) REVERT: B 77 LYS cc_start: 0.9303 (mtpt) cc_final: 0.8854 (tptt) REVERT: C 51 MET cc_start: 0.8506 (mmp) cc_final: 0.8252 (mmp) REVERT: C 57 TYR cc_start: 0.7602 (t80) cc_final: 0.6802 (t80) REVERT: C 81 ARG cc_start: 0.7635 (tpt170) cc_final: 0.7103 (tpt170) REVERT: C 95 LYS cc_start: 0.8869 (tmmt) cc_final: 0.8624 (ttmt) REVERT: D 108 LYS cc_start: 0.7998 (mttt) cc_final: 0.7434 (mmtm) REVERT: E 74 ILE cc_start: 0.9210 (tt) cc_final: 0.8939 (mt) REVERT: E 79 LYS cc_start: 0.8148 (ptmm) cc_final: 0.7939 (pttt) REVERT: E 125 GLN cc_start: 0.8643 (mt0) cc_final: 0.8298 (mp10) REVERT: F 40 ARG cc_start: 0.7552 (ttp80) cc_final: 0.6734 (tpp80) REVERT: G 74 LYS cc_start: 0.8674 (mmtt) cc_final: 0.8207 (tppp) REVERT: G 84 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.8787 (tp-100) REVERT: H 93 GLU cc_start: 0.8005 (mp0) cc_final: 0.7589 (mp0) REVERT: K 35 ILE cc_start: 0.7169 (tt) cc_final: 0.6887 (tt) REVERT: K 47 GLU cc_start: 0.6402 (tm-30) cc_final: 0.5649 (pt0) REVERT: K 265 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7334 (mt) REVERT: K 283 MET cc_start: 0.5944 (mmm) cc_final: 0.4918 (tpp) REVERT: K 292 LYS cc_start: 0.5984 (mmpt) cc_final: 0.5349 (ptpt) REVERT: K 293 LEU cc_start: 0.7015 (OUTLIER) cc_final: 0.6320 (mp) REVERT: K 319 MET cc_start: 0.8475 (mmm) cc_final: 0.7704 (mmt) outliers start: 36 outliers final: 24 residues processed: 218 average time/residue: 0.1278 time to fit residues: 40.1443 Evaluate side-chains 207 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 180 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 84 GLN Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 207 VAL Chi-restraints excluded: chain K residue 239 PHE Chi-restraints excluded: chain K residue 265 LEU Chi-restraints excluded: chain K residue 293 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 119 optimal weight: 40.0000 chunk 50 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 74 optimal weight: 0.0170 chunk 1 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 overall best weight: 2.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 49 HIS ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN ** K 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.112308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.077473 restraints weight = 53474.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.079493 restraints weight = 25042.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.080713 restraints weight = 16398.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.081378 restraints weight = 13038.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.081688 restraints weight = 11644.575| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.7380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 15502 Z= 0.193 Angle : 0.717 10.125 22197 Z= 0.394 Chirality : 0.044 0.280 2514 Planarity : 0.005 0.063 1798 Dihedral : 30.485 169.118 4471 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.43 % Allowed : 27.35 % Favored : 69.21 % 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: 0.96 (0.25), residues: 1061 helix: 1.02 (0.20), residues: 680 sheet: 1.41 (0.86), residues: 42 loop : -0.07 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 79 TYR 0.059 0.003 TYR H 83 PHE 0.018 0.002 PHE E 67 TRP 0.011 0.002 TRP K 281 HIS 0.009 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.19 (15502) covalent geometry : angle 0.71721 / 0.39 (22197) hydrogen bonds : bond 0.05500 / 3.68 ( 837) hydrogen bonds : angle 3.65902 / 2.68 ( 2152) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 180 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8751 (tp30) cc_final: 0.8082 (tp30) REVERT: A 90 MET cc_start: 0.8830 (mmm) cc_final: 0.8625 (mmp) REVERT: B 63 GLU cc_start: 0.8401 (pt0) cc_final: 0.7899 (pt0) REVERT: B 77 LYS cc_start: 0.9315 (mtpt) cc_final: 0.8879 (tptt) REVERT: C 51 MET cc_start: 0.8684 (mmp) cc_final: 0.8270 (mmp) REVERT: C 95 LYS cc_start: 0.9019 (tmmt) cc_final: 0.8759 (ttmt) REVERT: D 108 LYS cc_start: 0.8017 (mttt) cc_final: 0.7445 (mmtm) REVERT: E 125 GLN cc_start: 0.8674 (mt0) cc_final: 0.8341 (mp10) REVERT: F 40 ARG cc_start: 0.7635 (ttp80) cc_final: 0.6736 (tpp80) REVERT: G 71 ARG cc_start: 0.8414 (mtt180) cc_final: 0.7598 (mtm110) REVERT: G 84 GLN cc_start: 0.9095 (OUTLIER) cc_final: 0.8855 (tp-100) REVERT: H 93 GLU cc_start: 0.8059 (mp0) cc_final: 0.7633 (mp0) REVERT: K 35 ILE cc_start: 0.7203 (tt) cc_final: 0.6909 (tt) REVERT: K 47 GLU cc_start: 0.6297 (tm-30) cc_final: 0.5548 (pt0) REVERT: K 283 MET cc_start: 0.6095 (mmm) cc_final: 0.5061 (tpp) REVERT: K 292 LYS cc_start: 0.6048 (mmpt) cc_final: 0.5475 (ptpt) REVERT: K 293 LEU cc_start: 0.6935 (OUTLIER) cc_final: 0.6306 (mp) REVERT: K 319 MET cc_start: 0.8475 (mmm) cc_final: 0.7710 (mmt) outliers start: 31 outliers final: 26 residues processed: 203 average time/residue: 0.1389 time to fit residues: 40.6026 Evaluate side-chains 204 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 176 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 84 GLN Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 207 VAL Chi-restraints excluded: chain K residue 239 PHE Chi-restraints excluded: chain K residue 293 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 22 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 55 optimal weight: 0.3980 chunk 120 optimal weight: 20.0000 chunk 77 optimal weight: 2.9990 chunk 108 optimal weight: 20.0000 chunk 34 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 87 optimal weight: 20.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.113352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.078530 restraints weight = 52214.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.080622 restraints weight = 24234.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.081835 restraints weight = 15757.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.082517 restraints weight = 12554.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.082826 restraints weight = 11215.013| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.7482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 15502 Z= 0.149 Angle : 0.678 12.248 22197 Z= 0.376 Chirality : 0.042 0.272 2514 Planarity : 0.005 0.061 1798 Dihedral : 30.415 169.252 4471 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.43 % Allowed : 27.46 % Favored : 69.10 % 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: 1.11 (0.26), residues: 1061 helix: 1.13 (0.20), residues: 681 sheet: 1.54 (0.89), residues: 42 loop : 0.01 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 79 TYR 0.067 0.003 TYR H 83 PHE 0.016 0.002 PHE E 67 TRP 0.008 0.001 TRP K 251 HIS 0.006 0.001 HIS K 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.15 (15502) covalent geometry : angle 0.67774 / 0.38 (22197) hydrogen bonds : bond 0.04888 / 3.29 ( 837) hydrogen bonds : angle 3.52041 / 2.57 ( 2152) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3120.65 seconds wall clock time: 54 minutes 22.95 seconds (3262.95 seconds total)