Starting phenix.real_space_refine on Fri Jul 3 13:26:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gmk_51449/07_2026/9gmk_51449.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gmk_51449/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9gmk_51449/07_2026/9gmk_51449.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gmk_51449/07_2026/9gmk_51449.map" model { file = "/net/cci-nas-00/data/ceres_data/9gmk_51449/07_2026/9gmk_51449.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gmk_51449/07_2026/9gmk_51449.cif" } 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-dev-6108/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: 2.55, per 1000 atoms: 0.17 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: 0.84 Conformation dependent library (CDL) restraints added in 315.4 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: 1.72 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: 2.15 Time building geometry restraints manager: 1.10 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: 21579 2.27 - 4.55: 542 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: 0.770 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: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.890 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.100 ------------------------------------------------------------------------------- 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 : 0.852 11.363 22197 Z= 0.657 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 0.85216 / 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 : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 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: 0.7901 (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: 0.7262 (ttp-110) 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: 0.6663 (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: 0.7240 (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: 0.7227 (mt) REVERT: E 68 GLN cc_start: 0.7660 (mp-120) cc_final: 0.6760 (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: 0.5158 (mp) REVERT: F 45 ARG cc_start: 0.6595 (tpt-90) cc_final: 0.5453 (mmm160) REVERT: F 47 SER cc_start: 0.7966 (t) cc_final: 0.7525 (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: 0.7254 (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: 0.5566 (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: 0.6283 (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: 0.1563 time to fit residues: 78.4112 Evaluate side-chains 201 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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: 5.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 9.9990 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: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 31 HIS ** 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** E 68 GLN E 85 GLN F 93 GLN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.123094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.090678 restraints weight = 54261.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.092818 restraints weight = 26769.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.094072 restraints weight = 17547.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.094798 restraints weight = 13838.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.095144 restraints weight = 12241.081| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.213 15502 Z= 0.309 Angle : 0.888 18.130 22197 Z= 0.496 Chirality : 0.052 0.283 2514 Planarity : 0.009 0.087 1798 Dihedral : 30.233 170.780 4471 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 18.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 4.54 % Allowed : 16.50 % Favored : 78.96 % 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: 0.05 (0.24), residues: 1061 helix: 0.31 (0.19), residues: 676 sheet: 0.67 (0.85), residues: 44 loop : -0.36 (0.31), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.002 ARG K 34 TYR 0.028 0.003 TYR B 98 PHE 0.035 0.004 PHE E 104 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 0.00663 / 0.31 (15502) covalent geometry : angle 0.88788 / 0.50 (22197) hydrogen bonds : bond 0.07482 / 4.94 ( 837) hydrogen bonds : angle 4.17891 / 3.01 ( 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: 41 poor density : 217 time to evaluate : 0.401 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: 0.8837 (tp30) cc_final: 0.8347 (tp30) REVERT: B 27 GLN cc_start: 0.8339 (mp10) cc_final: 0.8074 (mp10) REVERT: B 77 LYS cc_start: 0.9210 (mtpt) cc_final: 0.8729 (tptt) REVERT: C 81 ARG cc_start: 0.7300 (tpt170) cc_final: 0.6847 (tpp-160) REVERT: D 108 LYS cc_start: 0.7990 (mttt) cc_final: 0.7341 (mmtt) REVERT: E 53 ARG cc_start: 0.8480 (ptm160) cc_final: 0.8197 (ptp-170) REVERT: E 63 ARG cc_start: 0.7363 (mpt180) cc_final: 0.7043 (mmt180) REVERT: F 31 LYS cc_start: 0.9129 (tttt) cc_final: 0.8889 (tttm) REVERT: F 55 ARG cc_start: 0.8184 (mtt180) cc_final: 0.7959 (mtt-85) REVERT: F 85 ASP cc_start: 0.8988 (m-30) cc_final: 0.8770 (m-30) REVERT: G 38 ASN cc_start: 0.7409 (t0) cc_final: 0.6708 (t0) REVERT: K 18 ARG cc_start: 0.7991 (pmt-80) cc_final: 0.7631 (tpt90) REVERT: K 23 GLU cc_start: 0.8832 (tp30) cc_final: 0.8561 (tm-30) REVERT: K 47 GLU cc_start: 0.6162 (tm-30) cc_final: 0.5058 (pt0) REVERT: K 150 MET cc_start: 0.5650 (mmp) cc_final: 0.5418 (mmp) REVERT: K 283 MET cc_start: 0.5430 (mmm) cc_final: 0.4627 (mmm) REVERT: K 319 MET cc_start: 0.8564 (mmm) cc_final: 0.7758 (mmt) outliers start: 41 outliers final: 19 residues processed: 243 average time/residue: 0.1276 time to fit residues: 43.1969 Evaluate side-chains 186 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 167 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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 E residue 65 LEU 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 3 optimal weight: 0.1980 chunk 80 optimal weight: 20.0000 chunk 28 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 32 optimal weight: 0.2980 chunk 57 optimal weight: 0.9980 chunk 102 optimal weight: 30.0000 chunk 21 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 82 HIS E 68 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.125624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.092412 restraints weight = 52970.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.094728 restraints weight = 25226.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.096099 restraints weight = 16268.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.096875 restraints weight = 12680.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.097243 restraints weight = 11146.621| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.4022 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= 0.155 Angle : 0.659 8.821 22197 Z= 0.379 Chirality : 0.042 0.264 2514 Planarity : 0.005 0.073 1798 Dihedral : 30.233 170.374 4471 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.99 % Allowed : 19.49 % Favored : 77.52 % 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: 0.74 (0.25), residues: 1061 helix: 0.92 (0.20), residues: 672 sheet: 1.15 (0.89), residues: 42 loop : -0.27 (0.31), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 79 TYR 0.026 0.002 TYR D 40 PHE 0.019 0.002 PHE E 67 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 0.00281 / 0.16 (15502) covalent geometry : angle 0.65926 / 0.38 (22197) hydrogen bonds : bond 0.05368 / 3.61 ( 837) hydrogen bonds : angle 3.63665 / 2.65 ( 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 217 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 190 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8728 (tp30) cc_final: 0.8204 (tp30) REVERT: A 90 MET cc_start: 0.8548 (mmm) cc_final: 0.8206 (mmp) REVERT: B 77 LYS cc_start: 0.9175 (mtpt) cc_final: 0.8713 (tptt) REVERT: C 25 PHE cc_start: 0.7996 (m-80) cc_final: 0.7689 (m-80) REVERT: C 51 MET cc_start: 0.8462 (mmp) cc_final: 0.7909 (mmm) REVERT: D 47 GLN cc_start: 0.8417 (pp30) cc_final: 0.8217 (pp30) REVERT: D 69 ILE cc_start: 0.8965 (mm) cc_final: 0.8717 (mt) REVERT: D 79 ARG cc_start: 0.8256 (ttm110) cc_final: 0.7890 (ttm110) REVERT: D 99 ARG cc_start: 0.7128 (mtt90) cc_final: 0.6824 (ttm170) REVERT: D 108 LYS cc_start: 0.7740 (mttt) cc_final: 0.7136 (mmtt) REVERT: E 50 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7715 (tt0) REVERT: E 63 ARG cc_start: 0.7219 (mpt180) cc_final: 0.6569 (mmt90) REVERT: F 31 LYS cc_start: 0.9008 (tttt) cc_final: 0.8765 (tmtt) REVERT: F 53 GLU cc_start: 0.7833 (tt0) cc_final: 0.7595 (tt0) REVERT: F 55 ARG cc_start: 0.8084 (mtt180) cc_final: 0.7690 (mtt-85) REVERT: F 63 GLU cc_start: 0.7512 (pp20) cc_final: 0.7310 (pp20) REVERT: F 85 ASP cc_start: 0.9095 (m-30) cc_final: 0.8894 (m-30) REVERT: F 88 TYR cc_start: 0.8411 (m-10) cc_final: 0.8133 (m-10) REVERT: G 32 ARG cc_start: 0.7862 (tmm-80) cc_final: 0.7400 (ttp-170) REVERT: G 36 LYS cc_start: 0.8280 (mmtp) cc_final: 0.7981 (mmtm) REVERT: G 84 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.7289 (tm-30) REVERT: K 23 GLU cc_start: 0.8879 (tp30) cc_final: 0.8565 (tm-30) REVERT: K 47 GLU cc_start: 0.6134 (tm-30) cc_final: 0.5121 (pt0) REVERT: K 105 TYR cc_start: 0.7052 (m-80) cc_final: 0.6004 (m-10) REVERT: K 150 MET cc_start: 0.5293 (mmp) cc_final: 0.5083 (mmp) REVERT: K 283 MET cc_start: 0.5442 (mmm) cc_final: 0.4554 (mmm) REVERT: K 319 MET cc_start: 0.8460 (mmm) cc_final: 0.7707 (mmt) outliers start: 27 outliers final: 11 residues processed: 206 average time/residue: 0.1089 time to fit residues: 32.2426 Evaluate side-chains 183 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 170 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 87 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 H residue 88 THR Chi-restraints excluded: chain K residue 239 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 82 optimal weight: 0.2980 chunk 35 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 26 optimal weight: 7.9990 chunk 128 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 89 optimal weight: 0.0010 chunk 53 optimal weight: 3.9990 chunk 111 optimal weight: 20.0000 overall best weight: 1.2188 ------------------------------------------------------------------------------- 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 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.123975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.091052 restraints weight = 53711.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.093286 restraints weight = 25487.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.094603 restraints weight = 16428.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.095336 restraints weight = 12864.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.095666 restraints weight = 11314.774| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.4392 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= 0.153 Angle : 0.635 7.506 22197 Z= 0.365 Chirality : 0.042 0.265 2514 Planarity : 0.005 0.072 1798 Dihedral : 30.235 170.121 4471 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.99 % Allowed : 20.27 % Favored : 75.75 % 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: 1.03 (0.25), residues: 1061 helix: 1.14 (0.20), residues: 672 sheet: 1.27 (0.89), residues: 42 loop : -0.13 (0.31), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 21 TYR 0.030 0.002 TYR H 83 PHE 0.018 0.002 PHE E 67 TRP 0.009 0.001 TRP K 251 HIS 0.007 0.001 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.15 (15502) covalent geometry : angle 0.63496 / 0.36 (22197) hydrogen bonds : bond 0.05114 / 3.43 ( 837) hydrogen bonds : angle 3.48758 / 2.54 ( 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 232 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 196 time to evaluate : 0.260 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: 0.8761 (tp30) cc_final: 0.8417 (tp30) REVERT: A 90 MET cc_start: 0.8612 (mmm) cc_final: 0.8272 (mmp) REVERT: B 77 LYS cc_start: 0.9207 (mtpt) cc_final: 0.8778 (tptt) REVERT: C 57 TYR cc_start: 0.7316 (t80) cc_final: 0.6850 (t80) REVERT: D 79 ARG cc_start: 0.8266 (ttm110) cc_final: 0.8034 (ttm110) REVERT: D 89 ILE cc_start: 0.7440 (OUTLIER) cc_final: 0.7185 (tt) REVERT: D 99 ARG cc_start: 0.7353 (mtt90) cc_final: 0.7055 (ttm170) REVERT: D 108 LYS cc_start: 0.7690 (mttt) cc_final: 0.7103 (mmtt) REVERT: E 63 ARG cc_start: 0.7150 (mpt180) cc_final: 0.6703 (mmt180) REVERT: F 31 LYS cc_start: 0.9092 (tttt) cc_final: 0.8814 (tmtt) REVERT: F 53 GLU cc_start: 0.7965 (tt0) cc_final: 0.7716 (tt0) REVERT: G 32 ARG cc_start: 0.8000 (tmm-80) cc_final: 0.7776 (tmm-80) REVERT: G 36 LYS cc_start: 0.8385 (mmtp) cc_final: 0.8060 (mmtm) REVERT: H 79 ARG cc_start: 0.8416 (ttm-80) cc_final: 0.7986 (ttm-80) REVERT: K 23 GLU cc_start: 0.8838 (tp30) cc_final: 0.8520 (tm-30) REVERT: K 47 GLU cc_start: 0.6331 (tm-30) cc_final: 0.5353 (pt0) REVERT: K 105 TYR cc_start: 0.7200 (m-80) cc_final: 0.5934 (m-80) REVERT: K 150 MET cc_start: 0.5425 (mmp) cc_final: 0.4963 (mmp) REVERT: K 265 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7285 (mm) REVERT: K 283 MET cc_start: 0.5332 (mmm) cc_final: 0.4560 (mmm) REVERT: K 293 LEU cc_start: 0.7278 (OUTLIER) cc_final: 0.6501 (mp) REVERT: K 294 TYR cc_start: 0.9058 (m-80) cc_final: 0.8728 (m-80) REVERT: K 319 MET cc_start: 0.8421 (mmm) cc_final: 0.7742 (mmt) outliers start: 36 outliers final: 20 residues processed: 216 average time/residue: 0.1078 time to fit residues: 33.4979 Evaluate side-chains 192 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 169 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 105 GLU 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 49 VAL Chi-restraints excluded: chain C residue 61 GLU 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 65 LEU 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 H residue 56 SER Chi-restraints excluded: chain H residue 88 THR 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=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: 5.9990 chunk 8 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 105 optimal weight: 30.0000 chunk 91 optimal weight: 20.0000 chunk 97 optimal weight: 0.9980 chunk 102 optimal weight: 0.0970 overall best weight: 1.5782 ------------------------------------------------------------------------------- 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 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN ** H 49 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 = 0.4290 r_free = 0.4290 target = 0.122681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.088816 restraints weight = 54485.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.090938 restraints weight = 26989.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.092173 restraints weight = 17886.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.092800 restraints weight = 14288.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 63)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.093212 restraints weight = 12827.650| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.4743 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= 0.159 Angle : 0.638 9.673 22197 Z= 0.364 Chirality : 0.041 0.261 2514 Planarity : 0.005 0.041 1798 Dihedral : 30.234 169.949 4471 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 4.21 % Allowed : 22.70 % Favored : 73.09 % 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: 1.10 (0.25), residues: 1061 helix: 1.21 (0.20), residues: 671 sheet: 1.16 (0.88), residues: 42 loop : -0.12 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 35 TYR 0.063 0.002 TYR H 83 PHE 0.015 0.002 PHE E 67 TRP 0.011 0.002 TRP K 300 HIS 0.006 0.001 HIS K 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.16 (15502) covalent geometry : angle 0.63829 / 0.36 (22197) hydrogen bonds : bond 0.05014 / 3.37 ( 837) hydrogen bonds : angle 3.44462 / 2.51 ( 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 215 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 177 time to evaluate : 0.267 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: 0.8740 (tp30) cc_final: 0.8378 (tp30) REVERT: A 90 MET cc_start: 0.8689 (mmm) cc_final: 0.8346 (mmp) REVERT: B 77 LYS cc_start: 0.9233 (mtpt) cc_final: 0.8799 (tptt) REVERT: C 57 TYR cc_start: 0.7247 (t80) cc_final: 0.6884 (t80) REVERT: C 94 ASN cc_start: 0.8959 (t0) cc_final: 0.8353 (m110) REVERT: D 59 MET cc_start: 0.9167 (tpt) cc_final: 0.8536 (tpt) REVERT: D 79 ARG cc_start: 0.8280 (ttm110) cc_final: 0.8030 (ttm110) REVERT: D 99 ARG cc_start: 0.7500 (mtt90) cc_final: 0.6956 (mtt90) REVERT: D 108 LYS cc_start: 0.7711 (mttt) cc_final: 0.7083 (mmtt) REVERT: F 31 LYS cc_start: 0.9148 (tttt) cc_final: 0.8846 (tmtt) REVERT: F 53 GLU cc_start: 0.8131 (tt0) cc_final: 0.7833 (tt0) REVERT: G 32 ARG cc_start: 0.8099 (tmm-80) cc_final: 0.7863 (tmm-80) REVERT: G 36 LYS cc_start: 0.8387 (mmtp) cc_final: 0.8104 (mmtm) REVERT: G 84 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.7754 (tm-30) REVERT: K 23 GLU cc_start: 0.8836 (tp30) cc_final: 0.8602 (tm-30) REVERT: K 47 GLU cc_start: 0.6503 (tm-30) cc_final: 0.5568 (pt0) REVERT: K 150 MET cc_start: 0.5157 (mmp) cc_final: 0.4950 (mmp) REVERT: K 283 MET cc_start: 0.5358 (mmm) cc_final: 0.4598 (mmm) REVERT: K 293 LEU cc_start: 0.7316 (OUTLIER) cc_final: 0.6629 (mp) REVERT: K 319 MET cc_start: 0.8537 (mmm) cc_final: 0.7880 (mmt) outliers start: 38 outliers final: 22 residues processed: 200 average time/residue: 0.1115 time to fit residues: 32.0541 Evaluate side-chains 190 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU 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 49 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 86 VAL 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 89 ILE Chi-restraints excluded: chain H residue 90 THR 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: 4.9990 chunk 94 optimal weight: 40.0000 chunk 129 optimal weight: 20.0000 chunk 21 optimal weight: 0.9990 chunk 127 optimal weight: 20.0000 chunk 15 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 82 optimal weight: 6.9990 chunk 45 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.122341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.088676 restraints weight = 53223.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.090873 restraints weight = 25399.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.092195 restraints weight = 16563.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.092944 restraints weight = 13045.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.093275 restraints weight = 11500.502| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.5032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 15502 Z= 0.146 Angle : 0.622 7.298 22197 Z= 0.356 Chirality : 0.041 0.327 2514 Planarity : 0.004 0.042 1798 Dihedral : 30.231 170.029 4471 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.43 % Allowed : 23.70 % Favored : 72.87 % 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: 1.24 (0.25), residues: 1061 helix: 1.30 (0.20), residues: 671 sheet: 1.11 (0.89), residues: 42 loop : -0.01 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG K 11 TYR 0.066 0.002 TYR H 83 PHE 0.016 0.001 PHE E 67 TRP 0.011 0.002 TRP K 281 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.15 (15502) covalent geometry : angle 0.62243 / 0.36 (22197) hydrogen bonds : bond 0.04815 / 3.24 ( 837) hydrogen bonds : angle 3.42330 / 2.50 ( 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 210 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 179 time to evaluate : 0.376 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: 0.8722 (tp30) cc_final: 0.8345 (tp30) REVERT: A 90 MET cc_start: 0.8695 (mmm) cc_final: 0.8461 (mmp) REVERT: B 77 LYS cc_start: 0.9242 (mtpt) cc_final: 0.8802 (tptt) REVERT: C 94 ASN cc_start: 0.8947 (t0) cc_final: 0.8332 (m110) REVERT: D 79 ARG cc_start: 0.8253 (ttm110) cc_final: 0.8002 (ttm110) REVERT: D 108 LYS cc_start: 0.7707 (mttt) cc_final: 0.7115 (mmtt) REVERT: E 74 ILE cc_start: 0.9087 (tt) cc_final: 0.8834 (mt) REVERT: F 31 LYS cc_start: 0.9246 (tttt) cc_final: 0.8867 (tmtt) REVERT: F 40 ARG cc_start: 0.6756 (ttm170) cc_final: 0.6306 (tpp80) REVERT: F 53 GLU cc_start: 0.8152 (tt0) cc_final: 0.7854 (tt0) REVERT: G 32 ARG cc_start: 0.8145 (tmm-80) cc_final: 0.7913 (tmm-80) REVERT: G 36 LYS cc_start: 0.8480 (mmtp) cc_final: 0.8188 (mmtm) REVERT: G 51 MET cc_start: 0.8490 (mmp) cc_final: 0.8033 (mmm) REVERT: H 113 GLU cc_start: 0.7151 (tm-30) cc_final: 0.6914 (tm-30) REVERT: K 23 GLU cc_start: 0.8829 (tp30) cc_final: 0.8541 (tm-30) REVERT: K 47 GLU cc_start: 0.6403 (tm-30) cc_final: 0.5481 (pt0) REVERT: K 150 MET cc_start: 0.5256 (mmp) cc_final: 0.5019 (mmp) REVERT: K 265 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7264 (mt) REVERT: K 283 MET cc_start: 0.5386 (mmm) cc_final: 0.4635 (mmm) REVERT: K 293 LEU cc_start: 0.6917 (OUTLIER) cc_final: 0.6223 (mp) outliers start: 31 outliers final: 19 residues processed: 197 average time/residue: 0.1046 time to fit residues: 29.7712 Evaluate side-chains 190 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 169 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 54 THR 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 39 ILE Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 79 ILE 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 89 ILE Chi-restraints excluded: chain H residue 90 THR 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: 10.0000 chunk 66 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 102 optimal weight: 8.9990 chunk 86 optimal weight: 30.0000 chunk 107 optimal weight: 20.0000 chunk 42 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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** ** 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 = 0.4168 r_free = 0.4168 target = 0.114163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.078763 restraints weight = 53827.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.080810 restraints weight = 26188.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.081982 restraints weight = 17479.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.082651 restraints weight = 14102.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.082986 restraints weight = 12598.585| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.6330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.158 15502 Z= 0.263 Angle : 0.802 11.118 22197 Z= 0.445 Chirality : 0.048 0.298 2514 Planarity : 0.007 0.090 1798 Dihedral : 30.498 170.397 4471 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 20.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.76 % Allowed : 22.59 % Favored : 72.65 % 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: 0.62 (0.25), residues: 1061 helix: 0.76 (0.20), residues: 668 sheet: 1.06 (0.84), residues: 44 loop : -0.15 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 11 TYR 0.095 0.004 TYR H 83 PHE 0.025 0.003 PHE E 67 TRP 0.008 0.002 TRP K 306 HIS 0.016 0.003 HIS H 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.26 (15502) covalent geometry : angle 0.80166 / 0.44 (22197) hydrogen bonds : bond 0.07210 / 4.81 ( 837) hydrogen bonds : angle 3.92348 / 2.89 ( 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 223 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 180 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8858 (tp30) cc_final: 0.8174 (tp30) REVERT: A 90 MET cc_start: 0.8826 (mmm) cc_final: 0.8544 (mmp) REVERT: B 77 LYS cc_start: 0.9321 (mtpt) cc_final: 0.8926 (tptt) REVERT: C 94 ASN cc_start: 0.9115 (t0) cc_final: 0.8899 (t0) REVERT: D 79 ARG cc_start: 0.8334 (ttm110) cc_final: 0.7941 (ttm110) REVERT: D 99 ARG cc_start: 0.7861 (mtt90) cc_final: 0.7638 (mtm110) REVERT: D 108 LYS cc_start: 0.7997 (mttt) cc_final: 0.7421 (mmtm) REVERT: E 53 ARG cc_start: 0.8556 (ptm160) cc_final: 0.8296 (ptp-170) REVERT: F 31 LYS cc_start: 0.9381 (tttt) cc_final: 0.8984 (tmtt) REVERT: G 36 LYS cc_start: 0.9048 (mmtp) cc_final: 0.8817 (mmtm) REVERT: G 38 ASN cc_start: 0.8889 (p0) cc_final: 0.8685 (p0) REVERT: G 57 TYR cc_start: 0.7899 (t80) cc_final: 0.7555 (t80) REVERT: G 74 LYS cc_start: 0.8690 (mmtt) cc_final: 0.8082 (tppp) REVERT: G 84 GLN cc_start: 0.9063 (OUTLIER) cc_final: 0.7992 (tm-30) REVERT: K 47 GLU cc_start: 0.6325 (tm-30) cc_final: 0.5509 (pt0) REVERT: K 150 MET cc_start: 0.5616 (mmp) cc_final: 0.5352 (mmp) REVERT: K 190 MET cc_start: 0.0310 (tpt) cc_final: 0.0083 (tpt) REVERT: K 283 MET cc_start: 0.5732 (mmm) cc_final: 0.4566 (tpp) REVERT: K 292 LYS cc_start: 0.6036 (mmpt) cc_final: 0.5394 (ptpt) REVERT: K 293 LEU cc_start: 0.7210 (OUTLIER) cc_final: 0.6572 (mp) outliers start: 43 outliers final: 27 residues processed: 209 average time/residue: 0.1071 time to fit residues: 32.0658 Evaluate side-chains 195 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 166 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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 50 ILE Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 96 THR 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 85 ASP 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 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 80 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 111 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 54 optimal weight: 0.5980 chunk 80 optimal weight: 20.0000 chunk 108 optimal weight: 20.0000 chunk 122 optimal weight: 20.0000 chunk 2 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 116 optimal weight: 30.0000 chunk 17 optimal weight: 10.0000 chunk 84 optimal weight: 8.9990 chunk 87 optimal weight: 20.0000 chunk 75 optimal weight: 10.0000 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.112474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.077445 restraints weight = 53805.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.079527 restraints weight = 25339.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.080721 restraints weight = 16676.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.081405 restraints weight = 13388.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.081711 restraints weight = 11922.878| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.7071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 15502 Z= 0.255 Angle : 0.751 9.552 22197 Z= 0.419 Chirality : 0.047 0.269 2514 Planarity : 0.006 0.080 1798 Dihedral : 30.650 169.447 4471 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.99 % Allowed : 25.91 % 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: 0.77 (0.25), residues: 1061 helix: 0.90 (0.20), residues: 669 sheet: 1.34 (0.85), residues: 42 loop : -0.16 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 79 TYR 0.106 0.004 TYR H 83 PHE 0.018 0.002 PHE E 67 TRP 0.008 0.002 TRP K 300 HIS 0.008 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.26 (15502) covalent geometry : angle 0.75104 / 0.42 (22197) hydrogen bonds : bond 0.05688 / 3.80 ( 837) hydrogen bonds : angle 3.81879 / 2.80 ( 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 223 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 187 time to evaluate : 0.280 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: 0.8757 (tp30) cc_final: 0.8108 (tp30) REVERT: A 56 LYS cc_start: 0.8546 (tttp) cc_final: 0.8314 (tmtt) REVERT: A 90 MET cc_start: 0.8816 (mmm) cc_final: 0.8561 (mmp) REVERT: A 105 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7070 (pm20) REVERT: B 63 GLU cc_start: 0.8444 (pt0) cc_final: 0.7918 (pt0) REVERT: B 77 LYS cc_start: 0.9325 (mtpt) cc_final: 0.8890 (tptt) REVERT: C 95 LYS cc_start: 0.8824 (tmmt) cc_final: 0.8537 (ttmt) REVERT: D 79 ARG cc_start: 0.8215 (ttm110) cc_final: 0.7780 (ttm110) REVERT: D 108 LYS cc_start: 0.8039 (mttt) cc_final: 0.7474 (mmtm) REVERT: E 74 ILE cc_start: 0.9196 (tt) cc_final: 0.8957 (mt) REVERT: E 93 GLN cc_start: 0.7813 (tp-100) cc_final: 0.7444 (tp40) REVERT: F 31 LYS cc_start: 0.9370 (tttt) cc_final: 0.9136 (tttm) REVERT: F 40 ARG cc_start: 0.7771 (ttp80) cc_final: 0.6851 (tpp80) REVERT: F 95 ARG cc_start: 0.8634 (mtt-85) cc_final: 0.8341 (ttm-80) REVERT: G 36 LYS cc_start: 0.9013 (mmtp) cc_final: 0.8758 (mmtm) REVERT: G 38 ASN cc_start: 0.8985 (p0) cc_final: 0.8768 (p0) REVERT: G 71 ARG cc_start: 0.8483 (mtt180) cc_final: 0.7756 (mtm110) REVERT: G 74 LYS cc_start: 0.8727 (mmtt) cc_final: 0.8501 (pttt) REVERT: H 93 GLU cc_start: 0.8082 (mp0) cc_final: 0.7763 (mp0) REVERT: K 47 GLU cc_start: 0.6288 (tm-30) cc_final: 0.5509 (pt0) REVERT: K 190 MET cc_start: 0.0463 (tpt) cc_final: 0.0236 (tpt) REVERT: K 283 MET cc_start: 0.5847 (mmm) cc_final: 0.4737 (tpp) REVERT: K 292 LYS cc_start: 0.6000 (mmpt) cc_final: 0.5370 (ptpt) REVERT: K 293 LEU cc_start: 0.6972 (OUTLIER) cc_final: 0.6386 (mp) outliers start: 36 outliers final: 26 residues processed: 211 average time/residue: 0.1147 time to fit residues: 34.9014 Evaluate side-chains 200 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL 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 54 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 85 ASP 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 83 TYR Chi-restraints excluded: chain H residue 90 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 54 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 chunk 121 optimal weight: 20.0000 chunk 11 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 80 optimal weight: 9.9990 chunk 21 optimal weight: 0.8980 chunk 127 optimal weight: 20.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN D 49 HIS ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN G 110 ASN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.114742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.079712 restraints weight = 53352.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.081830 restraints weight = 24998.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.083043 restraints weight = 16388.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.083750 restraints weight = 13135.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.084045 restraints weight = 11708.677| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.7116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15502 Z= 0.150 Angle : 0.694 11.731 22197 Z= 0.385 Chirality : 0.043 0.254 2514 Planarity : 0.005 0.045 1798 Dihedral : 30.571 170.109 4471 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.66 % Allowed : 27.80 % Favored : 69.55 % 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: 0.90 (0.25), residues: 1061 helix: 0.99 (0.20), residues: 669 sheet: 1.09 (0.86), residues: 44 loop : -0.04 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 79 TYR 0.102 0.003 TYR H 83 PHE 0.020 0.002 PHE E 67 TRP 0.008 0.002 TRP K 251 HIS 0.009 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.15 (15502) covalent geometry : angle 0.69357 / 0.39 (22197) hydrogen bonds : bond 0.04971 / 3.32 ( 837) hydrogen bonds : angle 3.62363 / 2.66 ( 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 219 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 195 time to evaluate : 0.255 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: 0.8710 (tp30) cc_final: 0.8082 (tp30) REVERT: A 90 MET cc_start: 0.8817 (mmm) cc_final: 0.8558 (mmp) REVERT: B 77 LYS cc_start: 0.9284 (mtpt) cc_final: 0.8912 (tptt) REVERT: C 81 ARG cc_start: 0.7450 (tpt170) cc_final: 0.6996 (tpt170) REVERT: C 95 LYS cc_start: 0.9014 (tmmt) cc_final: 0.8752 (ttmt) REVERT: D 47 GLN cc_start: 0.8517 (pp30) cc_final: 0.8079 (pt0) REVERT: D 79 ARG cc_start: 0.8136 (ttm110) cc_final: 0.7735 (ttm110) REVERT: D 108 LYS cc_start: 0.7990 (mttt) cc_final: 0.7418 (mmtm) REVERT: E 74 ILE cc_start: 0.9226 (tt) cc_final: 0.8947 (mt) REVERT: E 125 GLN cc_start: 0.8629 (mt0) cc_final: 0.8317 (mp10) REVERT: F 31 LYS cc_start: 0.9384 (tttt) cc_final: 0.9128 (tttm) REVERT: F 40 ARG cc_start: 0.7694 (ttp80) cc_final: 0.6836 (tpp80) REVERT: F 95 ARG cc_start: 0.8474 (mtt-85) cc_final: 0.8232 (ttm-80) REVERT: G 36 LYS cc_start: 0.8785 (mmtp) cc_final: 0.8506 (mmtm) REVERT: G 38 ASN cc_start: 0.8870 (p0) cc_final: 0.8543 (p0) REVERT: K 47 GLU cc_start: 0.6466 (tm-30) cc_final: 0.5687 (pt0) REVERT: K 150 MET cc_start: 0.5783 (mmm) cc_final: 0.5398 (mmm) REVERT: K 190 MET cc_start: 0.0482 (tpt) cc_final: 0.0268 (tpt) REVERT: K 283 MET cc_start: 0.5975 (mmm) cc_final: 0.4345 (tmm) REVERT: K 292 LYS cc_start: 0.5990 (mmpt) cc_final: 0.5434 (ptpt) REVERT: K 293 LEU cc_start: 0.6920 (OUTLIER) cc_final: 0.6327 (mp) outliers start: 24 outliers final: 17 residues processed: 208 average time/residue: 0.1089 time to fit residues: 32.5592 Evaluate side-chains 191 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 173 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 96 THR 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 84 ASN Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain K residue 24 GLN 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 119 optimal weight: 40.0000 chunk 50 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 74 optimal weight: 0.0270 chunk 1 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 overall best weight: 1.3242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.114477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.079639 restraints weight = 53519.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.081740 restraints weight = 25254.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.082963 restraints weight = 16583.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.083622 restraints weight = 13233.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.083941 restraints weight = 11842.681| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.7186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 15502 Z= 0.159 Angle : 0.690 10.893 22197 Z= 0.384 Chirality : 0.044 0.326 2514 Planarity : 0.005 0.053 1798 Dihedral : 30.552 169.481 4471 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.77 % Allowed : 28.46 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.25), residues: 1061 helix: 1.01 (0.20), residues: 671 sheet: 1.37 (0.87), residues: 42 loop : -0.02 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 35 TYR 0.126 0.004 TYR H 83 PHE 0.019 0.002 PHE E 67 TRP 0.008 0.001 TRP K 251 HIS 0.013 0.002 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.16 (15502) covalent geometry : angle 0.68985 / 0.38 (22197) hydrogen bonds : bond 0.04983 / 3.35 ( 837) hydrogen bonds : angle 3.64806 / 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 203 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 178 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8726 (tp30) cc_final: 0.8096 (tp30) REVERT: A 90 MET cc_start: 0.8843 (mmm) cc_final: 0.8611 (mmp) REVERT: A 105 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.6876 (pm20) REVERT: B 63 GLU cc_start: 0.8249 (pt0) cc_final: 0.7753 (pt0) REVERT: B 77 LYS cc_start: 0.9310 (mtpt) cc_final: 0.8878 (tptt) REVERT: C 35 ARG cc_start: 0.8315 (mtt-85) cc_final: 0.8030 (mtt-85) REVERT: C 81 ARG cc_start: 0.7458 (tpt170) cc_final: 0.7004 (tpt170) REVERT: C 95 LYS cc_start: 0.9042 (tmmt) cc_final: 0.8724 (ttmt) REVERT: D 79 ARG cc_start: 0.8146 (ttm110) cc_final: 0.7727 (ttm110) REVERT: D 108 LYS cc_start: 0.7983 (mttt) cc_final: 0.7413 (mmtm) REVERT: E 74 ILE cc_start: 0.9198 (tt) cc_final: 0.8982 (mt) REVERT: E 125 GLN cc_start: 0.8640 (mt0) cc_final: 0.8311 (mp10) REVERT: F 31 LYS cc_start: 0.9389 (tttt) cc_final: 0.9126 (tttm) REVERT: F 40 ARG cc_start: 0.7745 (ttp80) cc_final: 0.6826 (tpp80) REVERT: G 36 LYS cc_start: 0.8825 (mmtp) cc_final: 0.8557 (mmtm) REVERT: G 38 ASN cc_start: 0.8863 (p0) cc_final: 0.8538 (p0) REVERT: G 71 ARG cc_start: 0.8322 (mtt180) cc_final: 0.7604 (mtm110) REVERT: H 93 GLU cc_start: 0.7890 (mp0) cc_final: 0.7554 (mp0) REVERT: K 47 GLU cc_start: 0.6546 (tm-30) cc_final: 0.5762 (pt0) REVERT: K 150 MET cc_start: 0.5525 (mmm) cc_final: 0.4589 (mpp) REVERT: K 190 MET cc_start: 0.0463 (tpt) cc_final: 0.0240 (tpt) REVERT: K 283 MET cc_start: 0.6005 (mmm) cc_final: 0.4360 (tmm) REVERT: K 292 LYS cc_start: 0.5956 (mmpt) cc_final: 0.5410 (ptpt) REVERT: K 293 LEU cc_start: 0.6863 (OUTLIER) cc_final: 0.6263 (mp) outliers start: 25 outliers final: 19 residues processed: 195 average time/residue: 0.1151 time to fit residues: 32.2190 Evaluate side-chains 196 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 175 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 83 TYR 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 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: 2.9990 chunk 97 optimal weight: 8.9990 chunk 55 optimal weight: 0.2980 chunk 120 optimal weight: 30.0000 chunk 77 optimal weight: 2.9990 chunk 108 optimal weight: 20.0000 chunk 34 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 54 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 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 = 0.4168 r_free = 0.4168 target = 0.114175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.079446 restraints weight = 52940.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.081569 restraints weight = 24837.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.082781 restraints weight = 16264.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.083446 restraints weight = 12991.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.083791 restraints weight = 11598.858| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.7248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 15502 Z= 0.162 Angle : 0.691 10.680 22197 Z= 0.384 Chirality : 0.043 0.308 2514 Planarity : 0.005 0.052 1798 Dihedral : 30.542 169.297 4471 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.66 % Allowed : 28.35 % Favored : 68.99 % 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: 1.04 (0.20), residues: 671 sheet: 1.37 (0.87), residues: 42 loop : -0.01 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 35 TYR 0.123 0.004 TYR H 83 PHE 0.017 0.001 PHE E 67 TRP 0.008 0.001 TRP K 251 HIS 0.011 0.002 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.16 (15502) covalent geometry : angle 0.69063 / 0.38 (22197) hydrogen bonds : bond 0.05004 / 3.38 ( 837) hydrogen bonds : angle 3.66234 / 2.69 ( 2152) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2724.18 seconds wall clock time: 47 minutes 18.94 seconds (2838.94 seconds total)