Starting phenix.real_space_refine on Thu Sep 18 05:30:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gmk_51449/09_2025/9gmk_51449.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gmk_51449/09_2025/9gmk_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_51449/09_2025/9gmk_51449.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gmk_51449/09_2025/9gmk_51449.map" model { file = "/net/cci-nas-00/data/ceres_data/9gmk_51449/09_2025/9gmk_51449.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gmk_51449/09_2025/9gmk_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-2.0-5805/lib/python3.9/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: 3.25, per 1000 atoms: 0.22 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: 1.21 Conformation dependent library (CDL) restraints added in 410.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2020 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 3 sheets defined 64.8% alpha, 2.2% beta 136 base pairs and 251 stacking pairs defined. Time for finding SS restraints: 2.20 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.794A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.588A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 50 through 76 removed outlier: 3.844A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.860A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 56 through 84 Processing helix chain 'D' and resid 90 through 102 removed outlier: 4.158A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU D 102 " --> pdb=" O VAL D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 124 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.572A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.786A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY E 132 " --> pdb=" O ARG E 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.545A pdb=" N GLY F 28 " --> pdb=" O ASN F 25 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 25 through 29' Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 50 through 76 removed outlier: 3.955A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.517A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.530A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 98 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 removed outlier: 4.006A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 124 removed outlier: 3.640A pdb=" N ALA H 124 " --> pdb=" O LYS H 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 11 through 38 removed outlier: 3.697A pdb=" N LYS K 38 " --> pdb=" O ARG K 34 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 54 Processing helix chain 'K' and resid 54 through 76 removed outlier: 3.637A pdb=" N VAL K 58 " --> pdb=" O SER K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 99 Processing helix chain 'K' and resid 107 through 114 Processing helix chain 'K' and resid 146 through 158 Processing helix chain 'K' and resid 171 through 176 Processing helix chain 'K' and resid 250 through 261 Processing helix chain 'K' and resid 271 through 277 removed outlier: 3.782A pdb=" N TYR K 277 " --> pdb=" O VAL K 273 " (cutoff:3.500A) Processing helix chain 'K' and resid 301 through 307 removed outlier: 3.683A pdb=" N ASP K 305 " --> pdb=" O THR K 301 " (cutoff:3.500A) Processing helix chain 'K' and resid 314 through 327 Processing helix chain 'K' and resid 338 through 344 removed outlier: 4.510A pdb=" N SER K 342 " --> pdb=" O ASP K 338 " (cutoff:3.500A) Processing helix chain 'K' and resid 350 through 355 removed outlier: 3.877A pdb=" N SER K 354 " --> pdb=" O GLY K 350 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.700A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'K' and resid 183 through 185 removed outlier: 6.318A pdb=" N VAL K 164 " --> pdb=" O SER K 184 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N VAL K 103 " --> pdb=" O LEU K 265 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N LEU K 267 " --> pdb=" O VAL K 103 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N TYR K 105 " --> pdb=" O LEU K 267 " (cutoff:3.500A) removed outlier: 9.974A pdb=" N LEU K 311 " --> pdb=" O LEU K 293 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ILE K 295 " --> pdb=" O LEU K 311 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 192 through 194 498 hydrogen bonds defined for protein. 1482 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 339 hydrogen bonds 670 hydrogen bond angles 0 basepair planarities 136 basepair parallelities 251 stacking parallelities Total time for adding SS restraints: 3.18 Time building geometry restraints manager: 1.62 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=" C ILE C 79 " pdb=" O ILE C 79 " ideal model delta sigma weight residual 1.238 1.253 -0.015 7.10e-03 1.98e+04 4.35e+00 bond pdb=" C GLY H 53 " pdb=" O GLY H 53 " ideal model delta sigma weight residual 1.232 1.249 -0.016 9.10e-03 1.21e+04 3.29e+00 bond pdb=" C LEU H 101 " pdb=" N LEU H 102 " ideal model delta sigma weight residual 1.332 1.298 0.034 1.92e-02 2.71e+03 3.05e+00 bond pdb=" CG ARG K 18 " pdb=" CD ARG K 18 " ideal model delta sigma weight residual 1.520 1.471 0.049 3.00e-02 1.11e+03 2.64e+00 bond pdb=" CG LEU A 126 " pdb=" CD1 LEU A 126 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.52e+00 ... (remaining 15497 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 21823 2.27 - 4.55: 298 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=" CA GLN A 93 " pdb=" CB GLN A 93 " pdb=" CG GLN A 93 " ideal model delta sigma weight residual 114.10 122.48 -8.38 2.00e+00 2.50e-01 1.76e+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: 2032 0.043 - 0.086: 372 0.086 - 0.129: 89 0.129 - 0.172: 14 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: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.870 Find NCS groups from input model: 0.150 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6531 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 : 0.004 0.055 15502 Z= 0.182 Angle : 0.739 11.363 22197 Z= 0.425 Chirality : 0.038 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 aren 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 covalent geometry : bond 0.00384 (15502) covalent geometry : angle 0.73928 (22197) hydrogen bonds : bond 0.11633 ( 837) hydrogen bonds : angle 5.20619 ( 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 : 0.466 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: 0.1839 time to fit residues: 90.5352 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 : 0.418 ------------------------------------------------------------------------------- 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: 8.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 40.0000 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 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... Flipped N/Q/H residues before XYZ refinement: C 31 HIS ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 85 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS K 24 GLN ** K 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 312 HIS ** 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 = 0.4236 r_free = 0.4236 target = 0.118205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.084169 restraints weight = 54742.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.086274 restraints weight = 26979.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.087517 restraints weight = 17890.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.088149 restraints weight = 14315.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.088547 restraints weight = 12832.025| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.4814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.099 15502 Z= 0.350 Angle : 0.846 10.664 22197 Z= 0.477 Chirality : 0.046 0.196 2514 Planarity : 0.009 0.104 1798 Dihedral : 30.059 174.195 4471 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 20.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 4.98 % Allowed : 16.50 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 aren not related in a simple way. whole: 0.07 (0.24), residues: 1061 helix: 0.24 (0.19), residues: 679 sheet: 1.12 (0.85), residues: 42 loop : -0.21 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.078 0.002 ARG K 30 TYR 0.040 0.004 TYR H 83 PHE 0.034 0.005 PHE E 104 TRP 0.013 0.002 TRP K 251 HIS 0.017 0.003 HIS H 49 Details of bonding type rmsd covalent geometry : bond 0.00783 (15502) covalent geometry : angle 0.84633 (22197) hydrogen bonds : bond 0.07294 ( 837) hydrogen bonds : angle 4.10277 ( 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 269 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 224 time to evaluate : 0.352 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: 0.8899 (tp30) cc_final: 0.8364 (tp30) REVERT: A 134 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.7299 (ptm160) REVERT: B 77 LYS cc_start: 0.9304 (mtpt) cc_final: 0.8847 (tptt) REVERT: B 84 MET cc_start: 0.8935 (mmm) cc_final: 0.8725 (mmm) REVERT: D 47 GLN cc_start: 0.8563 (pp30) cc_final: 0.8346 (pp30) REVERT: D 108 LYS cc_start: 0.7984 (mttt) cc_final: 0.7355 (mmtt) REVERT: E 53 ARG cc_start: 0.8420 (ptm160) cc_final: 0.8161 (ptp-170) REVERT: E 60 LEU cc_start: 0.8083 (mm) cc_final: 0.7418 (tp) REVERT: E 63 ARG cc_start: 0.7818 (mpt180) cc_final: 0.7469 (mmt180) REVERT: F 31 LYS cc_start: 0.9306 (tttt) cc_final: 0.8892 (tmtt) REVERT: F 55 ARG cc_start: 0.8520 (mtt180) cc_final: 0.8238 (mtt-85) REVERT: G 38 ASN cc_start: 0.7336 (t0) cc_final: 0.6620 (t0) REVERT: G 57 TYR cc_start: 0.7818 (t80) cc_final: 0.7598 (t80) REVERT: K 18 ARG cc_start: 0.8058 (pmt-80) cc_final: 0.7682 (tpt90) REVERT: K 23 GLU cc_start: 0.8927 (tp30) cc_final: 0.8618 (tm-30) REVERT: K 47 GLU cc_start: 0.6231 (tm-30) cc_final: 0.5192 (pt0) REVERT: K 283 MET cc_start: 0.5650 (mmm) cc_final: 0.4870 (mmm) REVERT: K 319 MET cc_start: 0.8528 (mmm) cc_final: 0.7577 (mmt) outliers start: 45 outliers final: 17 residues processed: 256 average time/residue: 0.1568 time to fit residues: 54.6644 Evaluate side-chains 190 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 172 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 80 LEU 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: 2.9990 chunk 80 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 57 optimal weight: 0.3980 chunk 102 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 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 68 GLN E 108 ASN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.121309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.087366 restraints weight = 54113.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.089613 restraints weight = 25622.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.090911 restraints weight = 16642.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.091634 restraints weight = 13187.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.091971 restraints weight = 11680.343| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.5102 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= 0.158 Angle : 0.629 10.554 22197 Z= 0.357 Chirality : 0.036 0.170 2514 Planarity : 0.005 0.042 1798 Dihedral : 29.961 173.290 4471 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 3.99 % Allowed : 19.71 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.25), residues: 1061 helix: 1.02 (0.20), residues: 673 sheet: 1.41 (0.89), residues: 42 loop : -0.04 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 79 TYR 0.035 0.002 TYR H 83 PHE 0.025 0.002 PHE D 65 TRP 0.009 0.001 TRP K 251 HIS 0.009 0.001 HIS H 49 Details of bonding type rmsd covalent geometry : bond 0.00343 (15502) covalent geometry : angle 0.62866 (22197) hydrogen bonds : bond 0.04828 ( 837) hydrogen bonds : angle 3.49422 ( 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 256 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 220 time to evaluate : 0.423 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: 0.8646 (tp30) cc_final: 0.8064 (tp30) REVERT: B 77 LYS cc_start: 0.9242 (mtpt) cc_final: 0.8799 (tptt) REVERT: C 25 PHE cc_start: 0.8572 (m-80) cc_final: 0.8190 (m-80) REVERT: D 47 GLN cc_start: 0.8417 (pp30) cc_final: 0.8099 (pp30) REVERT: D 68 ASP cc_start: 0.9018 (t0) cc_final: 0.8689 (t0) REVERT: D 79 ARG cc_start: 0.8225 (ttm110) cc_final: 0.7992 (ttm110) REVERT: D 108 LYS cc_start: 0.7842 (mttt) cc_final: 0.7238 (mmtt) REVERT: E 53 ARG cc_start: 0.8337 (ptm160) cc_final: 0.8061 (ptp-170) REVERT: E 63 ARG cc_start: 0.7670 (mpt180) cc_final: 0.7079 (mmt90) REVERT: E 125 GLN cc_start: 0.8649 (mt0) cc_final: 0.8355 (mp10) REVERT: F 53 GLU cc_start: 0.8166 (tt0) cc_final: 0.7946 (tt0) REVERT: F 55 ARG cc_start: 0.8383 (mtt180) cc_final: 0.8033 (mtt-85) REVERT: G 84 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8697 (tp-100) REVERT: H 93 GLU cc_start: 0.7700 (mp0) cc_final: 0.7452 (mt-10) REVERT: K 23 GLU cc_start: 0.8948 (tp30) cc_final: 0.8660 (tm-30) REVERT: K 47 GLU cc_start: 0.6428 (tm-30) cc_final: 0.5329 (pt0) REVERT: K 190 MET cc_start: 0.0526 (tpt) cc_final: 0.0252 (tpt) REVERT: K 283 MET cc_start: 0.5468 (mmm) cc_final: 0.4605 (mmm) REVERT: K 319 MET cc_start: 0.8365 (mmm) cc_final: 0.7722 (mmt) outliers start: 36 outliers final: 15 residues processed: 241 average time/residue: 0.1392 time to fit residues: 47.4715 Evaluate side-chains 199 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 183 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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 58 LEU Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 37 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 88 THR Chi-restraints excluded: chain H residue 90 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: 20.0000 chunk 35 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 128 optimal weight: 8.9990 chunk 17 optimal weight: 0.0470 chunk 89 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 111 optimal weight: 7.9990 overall best weight: 0.9880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 HIS ** 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 63 ASN H 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.120394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.085962 restraints weight = 53517.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.088181 restraints weight = 25442.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.089479 restraints weight = 16575.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.090205 restraints weight = 13082.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.090529 restraints weight = 11587.520| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.5479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15502 Z= 0.159 Angle : 0.603 9.427 22197 Z= 0.347 Chirality : 0.035 0.193 2514 Planarity : 0.004 0.043 1798 Dihedral : 29.823 173.341 4471 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.65 % Allowed : 21.59 % Favored : 74.75 % 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 aren not related in a simple way. whole: 1.20 (0.25), residues: 1061 helix: 1.20 (0.20), residues: 671 sheet: 1.45 (0.88), residues: 42 loop : 0.10 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 35 TYR 0.049 0.002 TYR H 83 PHE 0.026 0.002 PHE D 65 TRP 0.012 0.001 TRP K 300 HIS 0.007 0.001 HIS K 355 Details of bonding type rmsd covalent geometry : bond 0.00351 (15502) covalent geometry : angle 0.60268 (22197) hydrogen bonds : bond 0.04615 ( 837) hydrogen bonds : angle 3.39825 ( 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 234 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 201 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8703 (tp30) cc_final: 0.8075 (tp30) REVERT: B 68 ASP cc_start: 0.8549 (m-30) cc_final: 0.8144 (t0) REVERT: B 77 LYS cc_start: 0.9265 (mtpt) cc_final: 0.8882 (tptt) REVERT: B 84 MET cc_start: 0.8897 (mmm) cc_final: 0.8592 (mmm) REVERT: C 25 PHE cc_start: 0.8584 (m-80) cc_final: 0.8155 (m-80) REVERT: C 94 ASN cc_start: 0.8958 (t0) cc_final: 0.8238 (m-40) REVERT: D 47 GLN cc_start: 0.8506 (pp30) cc_final: 0.8160 (pp30) REVERT: D 68 ASP cc_start: 0.8982 (t0) cc_final: 0.8740 (t0) REVERT: D 89 ILE cc_start: 0.7482 (OUTLIER) cc_final: 0.7151 (tt) REVERT: D 95 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.7347 (tt0) REVERT: D 108 LYS cc_start: 0.7828 (mttt) cc_final: 0.7211 (mmtt) REVERT: E 50 GLU cc_start: 0.8159 (pt0) cc_final: 0.7669 (tt0) REVERT: E 54 TYR cc_start: 0.8533 (m-80) cc_final: 0.7704 (m-80) REVERT: E 63 ARG cc_start: 0.7434 (mpt180) cc_final: 0.7215 (mmt180) REVERT: E 74 ILE cc_start: 0.9179 (tt) cc_final: 0.8912 (mt) REVERT: E 125 GLN cc_start: 0.8600 (mt0) cc_final: 0.8316 (mp10) REVERT: F 40 ARG cc_start: 0.6552 (ttm170) cc_final: 0.6145 (tpp80) REVERT: F 53 GLU cc_start: 0.8217 (tt0) cc_final: 0.7969 (tt0) REVERT: F 55 ARG cc_start: 0.8445 (mtt180) cc_final: 0.8121 (mtt-85) REVERT: G 74 LYS cc_start: 0.8390 (mmtt) cc_final: 0.7994 (tppp) REVERT: H 63 ASN cc_start: 0.9022 (OUTLIER) cc_final: 0.8696 (t0) REVERT: H 79 ARG cc_start: 0.8510 (ttm-80) cc_final: 0.8198 (ttm-80) REVERT: K 23 GLU cc_start: 0.8909 (tp30) cc_final: 0.8607 (tm-30) REVERT: K 47 GLU cc_start: 0.6453 (tm-30) cc_final: 0.5652 (pt0) REVERT: K 283 MET cc_start: 0.5402 (mmm) cc_final: 0.4605 (mmm) REVERT: K 293 LEU cc_start: 0.7061 (OUTLIER) cc_final: 0.6379 (mp) REVERT: K 319 MET cc_start: 0.8481 (mmm) cc_final: 0.7775 (mmt) outliers start: 33 outliers final: 21 residues processed: 221 average time/residue: 0.1483 time to fit residues: 45.7590 Evaluate side-chains 207 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 182 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 95 GLN 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 29 ILE Chi-restraints excluded: chain F residue 37 LEU 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 63 ASN Chi-restraints excluded: chain H residue 64 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 94 optimal weight: 30.0000 chunk 90 optimal weight: 30.0000 chunk 87 optimal weight: 6.9990 chunk 92 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 75 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 105 optimal weight: 10.0000 chunk 91 optimal weight: 0.5980 chunk 97 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 overall best weight: 2.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** H 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.114486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.079422 restraints weight = 54156.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.081528 restraints weight = 25849.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.082746 restraints weight = 17078.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.083395 restraints weight = 13705.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.083725 restraints weight = 12290.737| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.6554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 15502 Z= 0.234 Angle : 0.667 8.342 22197 Z= 0.382 Chirality : 0.039 0.232 2514 Planarity : 0.006 0.069 1798 Dihedral : 29.980 173.434 4471 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 5.32 % Allowed : 20.60 % Favored : 74.09 % 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 aren not related in a simple way. whole: 1.07 (0.25), residues: 1061 helix: 1.07 (0.20), residues: 676 sheet: 1.07 (0.85), residues: 44 loop : 0.13 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 71 TYR 0.063 0.003 TYR H 83 PHE 0.025 0.003 PHE E 67 TRP 0.007 0.001 TRP K 251 HIS 0.007 0.002 HIS H 82 Details of bonding type rmsd covalent geometry : bond 0.00529 (15502) covalent geometry : angle 0.66685 (22197) hydrogen bonds : bond 0.05476 ( 837) hydrogen bonds : angle 3.56258 ( 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 237 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 189 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8794 (tp30) cc_final: 0.8150 (tp30) REVERT: B 68 ASP cc_start: 0.8744 (m-30) cc_final: 0.8420 (m-30) REVERT: B 77 LYS cc_start: 0.9316 (mtpt) cc_final: 0.8953 (tptt) REVERT: B 84 MET cc_start: 0.8870 (mmm) cc_final: 0.8652 (mmm) REVERT: D 47 GLN cc_start: 0.8676 (pp30) cc_final: 0.8291 (pp30) REVERT: D 108 LYS cc_start: 0.8079 (mttt) cc_final: 0.7462 (mmtm) REVERT: E 50 GLU cc_start: 0.8194 (pt0) cc_final: 0.7945 (pt0) REVERT: E 53 ARG cc_start: 0.8415 (ptm160) cc_final: 0.8209 (ptp-170) REVERT: E 97 GLU cc_start: 0.7520 (pp20) cc_final: 0.7275 (pp20) REVERT: F 53 GLU cc_start: 0.8511 (tt0) cc_final: 0.8003 (tt0) REVERT: F 55 ARG cc_start: 0.8644 (mtt180) cc_final: 0.8287 (mtt-85) REVERT: F 63 GLU cc_start: 0.8566 (tp30) cc_final: 0.8240 (tp30) REVERT: G 57 TYR cc_start: 0.7893 (t80) cc_final: 0.7377 (t80) REVERT: G 74 LYS cc_start: 0.8679 (mmtt) cc_final: 0.8177 (tppp) REVERT: H 93 GLU cc_start: 0.8039 (mp0) cc_final: 0.7694 (mp0) REVERT: K 11 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8320 (mmp80) REVERT: K 47 GLU cc_start: 0.6423 (tm-30) cc_final: 0.5645 (pt0) REVERT: K 190 MET cc_start: 0.0873 (tpt) cc_final: 0.0656 (tpt) REVERT: K 283 MET cc_start: 0.5703 (mmm) cc_final: 0.4427 (tpp) REVERT: K 292 LYS cc_start: 0.6069 (mmpt) cc_final: 0.5398 (ptpt) REVERT: K 293 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.6606 (mp) REVERT: K 319 MET cc_start: 0.8548 (mmm) cc_final: 0.7863 (mmt) outliers start: 48 outliers final: 27 residues processed: 218 average time/residue: 0.1410 time to fit residues: 43.4038 Evaluate side-chains 203 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 174 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR 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 B residue 43 VAL Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 85 GLN Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 54 VAL 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 64 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 239 PHE Chi-restraints excluded: chain K residue 293 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 68 optimal weight: 0.8980 chunk 94 optimal weight: 30.0000 chunk 129 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 127 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** H 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.116337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.082371 restraints weight = 52703.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.084531 restraints weight = 24379.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.085789 restraints weight = 15745.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.086481 restraints weight = 12465.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.086808 restraints weight = 11117.817| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.6724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15502 Z= 0.155 Angle : 0.603 7.484 22197 Z= 0.346 Chirality : 0.035 0.160 2514 Planarity : 0.004 0.045 1798 Dihedral : 29.918 173.769 4471 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 3.32 % Allowed : 23.37 % Favored : 73.31 % 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 aren not related in a simple way. whole: 1.37 (0.25), residues: 1061 helix: 1.32 (0.20), residues: 680 sheet: 1.40 (0.87), residues: 42 loop : 0.17 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 63 TYR 0.072 0.002 TYR H 83 PHE 0.023 0.002 PHE D 65 TRP 0.009 0.001 TRP K 251 HIS 0.006 0.001 HIS K 355 Details of bonding type rmsd covalent geometry : bond 0.00341 (15502) covalent geometry : angle 0.60335 (22197) hydrogen bonds : bond 0.04459 ( 837) hydrogen bonds : angle 3.35179 ( 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 225 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 195 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8737 (tp30) cc_final: 0.8112 (tp30) REVERT: A 106 ASP cc_start: 0.8721 (m-30) cc_final: 0.8498 (t0) REVERT: B 77 LYS cc_start: 0.9303 (mtpt) cc_final: 0.8956 (tptt) REVERT: C 25 PHE cc_start: 0.8605 (m-80) cc_final: 0.8146 (m-80) REVERT: C 61 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8575 (mm-30) REVERT: C 94 ASN cc_start: 0.9044 (t0) cc_final: 0.8372 (m110) REVERT: D 47 GLN cc_start: 0.8650 (pp30) cc_final: 0.8222 (pp30) REVERT: D 79 ARG cc_start: 0.7939 (ttm110) cc_final: 0.7509 (ttm110) REVERT: D 89 ILE cc_start: 0.7554 (OUTLIER) cc_final: 0.7235 (tt) REVERT: D 108 LYS cc_start: 0.8022 (mttt) cc_final: 0.7370 (mmtm) REVERT: E 54 TYR cc_start: 0.8700 (m-80) cc_final: 0.7655 (m-80) REVERT: E 74 ILE cc_start: 0.9240 (tt) cc_final: 0.9006 (mt) REVERT: E 85 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7637 (mt0) REVERT: E 125 GLN cc_start: 0.8564 (mt0) cc_final: 0.8249 (mp10) REVERT: F 40 ARG cc_start: 0.7654 (ttp80) cc_final: 0.6815 (tpp80) REVERT: F 53 GLU cc_start: 0.8344 (tt0) cc_final: 0.8042 (tt0) REVERT: F 55 ARG cc_start: 0.8540 (mtt180) cc_final: 0.8245 (mtt-85) REVERT: F 63 GLU cc_start: 0.8518 (tp30) cc_final: 0.8228 (tp30) REVERT: G 51 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.8435 (tpp) REVERT: G 71 ARG cc_start: 0.8443 (mtm-85) cc_final: 0.7629 (mtm110) REVERT: G 91 GLU cc_start: 0.7786 (tm-30) cc_final: 0.7463 (tm-30) REVERT: H 93 GLU cc_start: 0.7781 (mp0) cc_final: 0.7559 (mp0) REVERT: H 105 GLU cc_start: 0.6705 (tt0) cc_final: 0.6393 (tt0) REVERT: K 47 GLU cc_start: 0.6592 (tm-30) cc_final: 0.5874 (pt0) REVERT: K 150 MET cc_start: 0.5096 (mmp) cc_final: 0.4525 (mmm) REVERT: K 283 MET cc_start: 0.5820 (mmm) cc_final: 0.4675 (tpp) REVERT: K 292 LYS cc_start: 0.5952 (mmpt) cc_final: 0.5345 (ptpt) REVERT: K 293 LEU cc_start: 0.6918 (OUTLIER) cc_final: 0.6255 (mp) REVERT: K 319 MET cc_start: 0.8473 (mmm) cc_final: 0.7731 (mmt) outliers start: 30 outliers final: 18 residues processed: 214 average time/residue: 0.1361 time to fit residues: 41.5663 Evaluate side-chains 201 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 179 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 85 GLN Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain G residue 51 MET 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 90 THR Chi-restraints excluded: chain K residue 239 PHE 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: 7.9990 chunk 48 optimal weight: 4.9990 chunk 110 optimal weight: 8.9990 chunk 94 optimal weight: 40.0000 chunk 66 optimal weight: 8.9990 chunk 64 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 102 optimal weight: 0.0000 chunk 86 optimal weight: 8.9990 chunk 107 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.112922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.077806 restraints weight = 53678.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.079889 restraints weight = 25129.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.081107 restraints weight = 16540.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.081753 restraints weight = 13262.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.082105 restraints weight = 11911.598| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.7374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 15502 Z= 0.211 Angle : 0.651 9.344 22197 Z= 0.369 Chirality : 0.038 0.296 2514 Planarity : 0.005 0.062 1798 Dihedral : 30.016 173.358 4471 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 4.87 % Allowed : 22.92 % Favored : 72.20 % 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 aren not related in a simple way. whole: 1.38 (0.26), residues: 1061 helix: 1.37 (0.20), residues: 680 sheet: 1.42 (0.88), residues: 42 loop : 0.08 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 11 TYR 0.066 0.002 TYR H 83 PHE 0.023 0.002 PHE D 65 TRP 0.008 0.001 TRP K 251 HIS 0.007 0.002 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00476 (15502) covalent geometry : angle 0.65082 (22197) hydrogen bonds : bond 0.05182 ( 837) hydrogen bonds : angle 3.53057 ( 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 236 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 192 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8804 (tp30) cc_final: 0.8124 (tp30) REVERT: A 56 LYS cc_start: 0.8543 (tttp) cc_final: 0.8243 (tmtt) REVERT: A 106 ASP cc_start: 0.8657 (m-30) cc_final: 0.8364 (t0) REVERT: B 63 GLU cc_start: 0.8366 (pt0) cc_final: 0.7823 (pt0) REVERT: B 77 LYS cc_start: 0.9346 (mtpt) cc_final: 0.9013 (tptt) REVERT: C 81 ARG cc_start: 0.7556 (tpt170) cc_final: 0.7135 (tpt170) REVERT: C 95 LYS cc_start: 0.8816 (ttpt) cc_final: 0.8563 (ttmt) REVERT: D 47 GLN cc_start: 0.8687 (pp30) cc_final: 0.8300 (pp30) REVERT: D 79 ARG cc_start: 0.8112 (ttm110) cc_final: 0.7635 (ttm110) REVERT: D 108 LYS cc_start: 0.8101 (mttt) cc_final: 0.7420 (mmtm) REVERT: E 54 TYR cc_start: 0.8678 (m-80) cc_final: 0.7750 (m-80) REVERT: E 77 ASP cc_start: 0.8336 (OUTLIER) cc_final: 0.8076 (p0) REVERT: E 85 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7761 (mt0) REVERT: E 130 ILE cc_start: 0.9165 (mm) cc_final: 0.8893 (mm) REVERT: F 40 ARG cc_start: 0.7793 (ttp80) cc_final: 0.6975 (tpp80) REVERT: F 53 GLU cc_start: 0.8551 (tt0) cc_final: 0.8203 (tt0) REVERT: F 63 GLU cc_start: 0.8584 (tp30) cc_final: 0.8201 (tp30) REVERT: F 84 MET cc_start: 0.8549 (tpp) cc_final: 0.8343 (tpp) REVERT: G 71 ARG cc_start: 0.8373 (mtm-85) cc_final: 0.7574 (mtm110) REVERT: H 93 GLU cc_start: 0.8100 (mp0) cc_final: 0.7722 (mp0) REVERT: K 47 GLU cc_start: 0.6617 (tm-30) cc_final: 0.5915 (pt0) REVERT: K 190 MET cc_start: 0.1379 (tpt) cc_final: 0.1141 (tpt) REVERT: K 265 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7053 (mm) REVERT: K 283 MET cc_start: 0.6061 (mmm) cc_final: 0.4499 (tmm) REVERT: K 292 LYS cc_start: 0.5931 (mmpt) cc_final: 0.5391 (ptpt) REVERT: K 293 LEU cc_start: 0.6744 (OUTLIER) cc_final: 0.6151 (mp) REVERT: K 319 MET cc_start: 0.8476 (mmm) cc_final: 0.7745 (mmt) outliers start: 44 outliers final: 29 residues processed: 220 average time/residue: 0.1404 time to fit residues: 43.8022 Evaluate side-chains 212 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 179 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 85 GLN Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 71 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 64 SER Chi-restraints excluded: chain H residue 84 ASN 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 265 LEU 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: 4.9990 chunk 80 optimal weight: 10.0000 chunk 108 optimal weight: 8.9990 chunk 122 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 116 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 84 optimal weight: 9.9990 chunk 87 optimal weight: 8.9990 chunk 75 optimal weight: 8.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN ** D 84 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** K 25 GLN K 231 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.106300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.070927 restraints weight = 54034.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.072844 restraints weight = 25246.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.073999 restraints weight = 16720.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.074623 restraints weight = 13486.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.074889 restraints weight = 12143.150| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.8743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.093 15502 Z= 0.364 Angle : 0.834 16.010 22197 Z= 0.463 Chirality : 0.047 0.258 2514 Planarity : 0.006 0.067 1798 Dihedral : 30.477 172.345 4471 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 21.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 5.65 % Allowed : 22.37 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.25), residues: 1061 helix: 0.78 (0.20), residues: 680 sheet: 1.41 (0.87), residues: 42 loop : -0.19 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 39 TYR 0.074 0.004 TYR H 83 PHE 0.023 0.003 PHE D 65 TRP 0.006 0.001 TRP K 306 HIS 0.013 0.003 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00824 (15502) covalent geometry : angle 0.83363 (22197) hydrogen bonds : bond 0.06974 ( 837) hydrogen bonds : angle 4.19405 ( 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 243 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 192 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8914 (tp30) cc_final: 0.8178 (tp30) REVERT: A 56 LYS cc_start: 0.8713 (tttp) cc_final: 0.8423 (tmtt) REVERT: A 106 ASP cc_start: 0.8792 (m-30) cc_final: 0.8536 (t0) REVERT: B 63 GLU cc_start: 0.8522 (pt0) cc_final: 0.8079 (pt0) REVERT: B 77 LYS cc_start: 0.9362 (mtpt) cc_final: 0.9041 (tptt) REVERT: B 88 TYR cc_start: 0.8991 (m-80) cc_final: 0.8737 (m-80) REVERT: C 57 TYR cc_start: 0.8348 (t80) cc_final: 0.7827 (t80) REVERT: C 81 ARG cc_start: 0.7720 (tpt170) cc_final: 0.7314 (tpt170) REVERT: D 59 MET cc_start: 0.9250 (tpt) cc_final: 0.8739 (tpt) REVERT: E 53 ARG cc_start: 0.8406 (ptm160) cc_final: 0.8177 (ptp-170) REVERT: E 77 ASP cc_start: 0.8378 (OUTLIER) cc_final: 0.8120 (p0) REVERT: E 80 THR cc_start: 0.7444 (OUTLIER) cc_final: 0.7051 (t) REVERT: E 93 GLN cc_start: 0.8009 (tp-100) cc_final: 0.7627 (tp40) REVERT: F 44 LYS cc_start: 0.8551 (mppt) cc_final: 0.8243 (tttm) REVERT: F 54 THR cc_start: 0.9230 (OUTLIER) cc_final: 0.9021 (t) REVERT: F 63 GLU cc_start: 0.8756 (tp30) cc_final: 0.8524 (tp30) REVERT: G 38 ASN cc_start: 0.9173 (p0) cc_final: 0.8920 (p0) REVERT: G 51 MET cc_start: 0.8924 (OUTLIER) cc_final: 0.8473 (tpp) REVERT: G 71 ARG cc_start: 0.8504 (mtm-85) cc_final: 0.7672 (mtm110) REVERT: H 76 GLU cc_start: 0.8466 (tp30) cc_final: 0.8064 (tp30) REVERT: H 93 GLU cc_start: 0.8367 (mp0) cc_final: 0.7859 (mp0) REVERT: H 105 GLU cc_start: 0.8004 (tt0) cc_final: 0.7476 (tt0) REVERT: K 47 GLU cc_start: 0.6244 (tm-30) cc_final: 0.5593 (pt0) REVERT: K 190 MET cc_start: 0.1762 (tpt) cc_final: 0.1532 (tpt) REVERT: K 265 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7205 (mm) REVERT: K 280 LEU cc_start: 0.8823 (mt) cc_final: 0.8582 (pp) REVERT: K 283 MET cc_start: 0.6220 (mmm) cc_final: 0.5217 (tpp) REVERT: K 292 LYS cc_start: 0.6004 (mmpt) cc_final: 0.5458 (ptpt) REVERT: K 293 LEU cc_start: 0.6502 (OUTLIER) cc_final: 0.5848 (pp) REVERT: K 319 MET cc_start: 0.8496 (mmm) cc_final: 0.7823 (mmt) outliers start: 51 outliers final: 34 residues processed: 222 average time/residue: 0.1413 time to fit residues: 44.3363 Evaluate side-chains 216 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 176 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 51 MET 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 64 SER Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 207 VAL Chi-restraints excluded: chain K residue 239 PHE Chi-restraints excluded: chain K residue 265 LEU Chi-restraints excluded: chain K residue 293 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 54 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 96 optimal weight: 0.0970 chunk 89 optimal weight: 0.8980 chunk 121 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 21 optimal weight: 0.6980 chunk 127 optimal weight: 6.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS H 49 HIS ** K 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 355 HIS ** 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 = 0.4105 r_free = 0.4105 target = 0.110133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.075489 restraints weight = 53469.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.077541 restraints weight = 24458.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.078785 restraints weight = 15939.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.079458 restraints weight = 12699.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.079764 restraints weight = 11375.421| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.8672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15502 Z= 0.179 Angle : 0.680 13.786 22197 Z= 0.379 Chirality : 0.038 0.277 2514 Planarity : 0.005 0.058 1798 Dihedral : 30.313 172.403 4471 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.99 % Allowed : 25.25 % Favored : 70.76 % 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 aren not related in a simple way. whole: 1.18 (0.26), residues: 1061 helix: 1.22 (0.20), residues: 677 sheet: 1.24 (0.87), residues: 44 loop : -0.01 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 233 TYR 0.069 0.003 TYR H 83 PHE 0.021 0.002 PHE D 65 TRP 0.006 0.001 TRP K 251 HIS 0.015 0.002 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00399 (15502) covalent geometry : angle 0.68031 (22197) hydrogen bonds : bond 0.04749 ( 837) hydrogen bonds : angle 3.59044 ( 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 240 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 204 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8712 (tp30) cc_final: 0.8016 (tp30) REVERT: A 56 LYS cc_start: 0.8547 (tttp) cc_final: 0.8249 (tmtt) REVERT: A 105 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6916 (pm20) REVERT: A 106 ASP cc_start: 0.8690 (m-30) cc_final: 0.8350 (t0) REVERT: B 63 GLU cc_start: 0.8356 (pt0) cc_final: 0.7794 (pt0) REVERT: B 77 LYS cc_start: 0.9329 (mtpt) cc_final: 0.8981 (tptt) REVERT: C 25 PHE cc_start: 0.8607 (m-80) cc_final: 0.8110 (m-80) REVERT: C 57 TYR cc_start: 0.8174 (t80) cc_final: 0.7588 (t80) REVERT: C 81 ARG cc_start: 0.7614 (tpt170) cc_final: 0.7218 (tpt170) REVERT: C 104 GLN cc_start: 0.8551 (mp10) cc_final: 0.8110 (mm-40) REVERT: D 106 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7592 (tt) REVERT: E 125 GLN cc_start: 0.8517 (mt0) cc_final: 0.8071 (mp10) REVERT: E 130 ILE cc_start: 0.9247 (mm) cc_final: 0.8962 (mm) REVERT: F 53 GLU cc_start: 0.8624 (tt0) cc_final: 0.8318 (tt0) REVERT: F 63 GLU cc_start: 0.8590 (tp30) cc_final: 0.8376 (tp30) REVERT: F 84 MET cc_start: 0.8728 (tpp) cc_final: 0.8495 (tpp) REVERT: G 20 ARG cc_start: 0.8656 (ttm170) cc_final: 0.8380 (ttm170) REVERT: G 51 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8731 (tpp) REVERT: G 57 TYR cc_start: 0.7842 (t80) cc_final: 0.7410 (t80) REVERT: G 71 ARG cc_start: 0.8341 (mtm-85) cc_final: 0.7596 (mtm110) REVERT: H 79 ARG cc_start: 0.8662 (tpp80) cc_final: 0.8372 (ttt90) REVERT: H 93 GLU cc_start: 0.8169 (mp0) cc_final: 0.7535 (mp0) REVERT: H 105 GLU cc_start: 0.7637 (tt0) cc_final: 0.7191 (tt0) REVERT: K 47 GLU cc_start: 0.6409 (tm-30) cc_final: 0.5661 (pt0) REVERT: K 218 ARG cc_start: 0.7476 (mpp80) cc_final: 0.6578 (mmm160) REVERT: K 265 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7097 (mm) REVERT: K 283 MET cc_start: 0.6235 (mmm) cc_final: 0.4641 (tmm) REVERT: K 292 LYS cc_start: 0.5985 (mmpt) cc_final: 0.5510 (ptpt) REVERT: K 293 LEU cc_start: 0.6239 (OUTLIER) cc_final: 0.5683 (pp) REVERT: K 319 MET cc_start: 0.8445 (mmm) cc_final: 0.7729 (mmt) outliers start: 36 outliers final: 23 residues processed: 226 average time/residue: 0.1413 time to fit residues: 45.1987 Evaluate side-chains 214 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 186 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain G residue 51 MET 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 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 265 LEU Chi-restraints excluded: chain K residue 293 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 119 optimal weight: 10.0000 chunk 50 optimal weight: 0.7980 chunk 52 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 84 optimal weight: 50.0000 chunk 12 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 93 GLN H 84 ASN ** K 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 173 HIS K 219 HIS ** K 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.108306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.073137 restraints weight = 54339.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.075092 restraints weight = 25252.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.076255 restraints weight = 16683.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.076899 restraints weight = 13457.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.077164 restraints weight = 12123.568| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.8946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 15502 Z= 0.241 Angle : 0.718 13.074 22197 Z= 0.398 Chirality : 0.040 0.237 2514 Planarity : 0.005 0.061 1798 Dihedral : 30.243 171.567 4471 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 4.10 % Allowed : 25.91 % Favored : 69.99 % 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 aren not related in a simple way. whole: 1.12 (0.26), residues: 1061 helix: 1.09 (0.20), residues: 677 sheet: 1.21 (0.86), residues: 44 loop : 0.17 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 95 TYR 0.065 0.003 TYR H 83 PHE 0.021 0.002 PHE D 65 TRP 0.006 0.001 TRP K 251 HIS 0.012 0.002 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00551 (15502) covalent geometry : angle 0.71803 (22197) hydrogen bonds : bond 0.05348 ( 837) hydrogen bonds : angle 3.73033 ( 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 231 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 194 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8822 (tp30) cc_final: 0.8126 (tp30) REVERT: A 56 LYS cc_start: 0.8632 (tttp) cc_final: 0.8320 (tmtt) REVERT: A 105 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.6931 (pm20) REVERT: A 106 ASP cc_start: 0.8636 (m-30) cc_final: 0.8243 (t0) REVERT: B 63 GLU cc_start: 0.8427 (pt0) cc_final: 0.7921 (pt0) REVERT: B 77 LYS cc_start: 0.9337 (mtpt) cc_final: 0.9011 (tptt) REVERT: C 57 TYR cc_start: 0.8191 (t80) cc_final: 0.7615 (t80) REVERT: C 81 ARG cc_start: 0.7607 (tpt170) cc_final: 0.7208 (tpt170) REVERT: C 104 GLN cc_start: 0.8514 (mp10) cc_final: 0.8200 (mm-40) REVERT: D 108 LYS cc_start: 0.8069 (pttt) cc_final: 0.7803 (pttt) REVERT: E 77 ASP cc_start: 0.8288 (OUTLIER) cc_final: 0.8063 (p0) REVERT: E 125 GLN cc_start: 0.8519 (mt0) cc_final: 0.8082 (mp10) REVERT: E 130 ILE cc_start: 0.9297 (mm) cc_final: 0.8934 (mm) REVERT: F 44 LYS cc_start: 0.8456 (mppt) cc_final: 0.8048 (tttm) REVERT: G 20 ARG cc_start: 0.8704 (ttm170) cc_final: 0.8454 (ttm170) REVERT: G 51 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8732 (tpp) REVERT: G 71 ARG cc_start: 0.8406 (mtm-85) cc_final: 0.7641 (mtm110) REVERT: H 93 GLU cc_start: 0.8290 (mp0) cc_final: 0.7626 (mp0) REVERT: H 105 GLU cc_start: 0.7796 (tt0) cc_final: 0.7355 (tt0) REVERT: K 47 GLU cc_start: 0.6395 (tm-30) cc_final: 0.5642 (pt0) REVERT: K 217 HIS cc_start: 0.5374 (t70) cc_final: 0.4939 (t70) REVERT: K 265 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7095 (mm) REVERT: K 283 MET cc_start: 0.6328 (mmm) cc_final: 0.4682 (tmm) REVERT: K 292 LYS cc_start: 0.6014 (mmpt) cc_final: 0.5533 (ptpt) REVERT: K 293 LEU cc_start: 0.6210 (OUTLIER) cc_final: 0.5650 (pp) REVERT: K 319 MET cc_start: 0.8481 (mmm) cc_final: 0.7738 (mmt) outliers start: 37 outliers final: 30 residues processed: 214 average time/residue: 0.1404 time to fit residues: 42.7391 Evaluate side-chains 219 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 184 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 51 MET 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 84 ASN Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 173 HIS Chi-restraints excluded: chain K residue 207 VAL Chi-restraints excluded: chain K residue 239 PHE Chi-restraints excluded: chain K residue 265 LEU Chi-restraints excluded: chain K residue 293 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 22 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 chunk 120 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 108 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 173 HIS K 219 HIS ** K 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.109203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.074072 restraints weight = 53707.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.076067 restraints weight = 24700.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.077233 restraints weight = 16277.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.077880 restraints weight = 13160.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.078161 restraints weight = 11880.756| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.8948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.179 15502 Z= 0.323 Angle : 1.022 59.200 22197 Z= 0.644 Chirality : 0.049 1.035 2514 Planarity : 0.006 0.113 1798 Dihedral : 30.254 171.568 4471 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 20.38 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.54 % Favored : 97.27 % Rotamer: Outliers : 4.10 % Allowed : 26.25 % Favored : 69.66 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 aren not related in a simple way. whole: 1.05 (0.26), residues: 1061 helix: 1.06 (0.20), residues: 683 sheet: 1.21 (0.86), residues: 44 loop : 0.05 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 95 TYR 0.062 0.004 TYR H 83 PHE 0.074 0.003 PHE E 67 TRP 0.006 0.001 TRP K 251 HIS 0.173 0.006 HIS K 173 Details of bonding type rmsd covalent geometry : bond 0.00649 (15502) covalent geometry : angle 1.02177 (22197) hydrogen bonds : bond 0.05444 ( 837) hydrogen bonds : angle 3.72469 ( 2152) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3464.60 seconds wall clock time: 60 minutes 12.58 seconds (3612.58 seconds total)