Starting phenix.real_space_refine on Fri May 16 11:13:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gmk_51449/05_2025/9gmk_51449.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gmk_51449/05_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_51449/05_2025/9gmk_51449.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gmk_51449/05_2025/9gmk_51449.map" model { file = "/net/cci-nas-00/data/ceres_data/9gmk_51449/05_2025/9gmk_51449.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gmk_51449/05_2025/9gmk_51449.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 8.21, per 1000 atoms: 0.56 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: 3.37 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 6.19 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.794A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.588A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 50 through 76 removed outlier: 3.844A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.860A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 56 through 84 Processing helix chain 'D' and resid 90 through 102 removed outlier: 4.158A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU D 102 " --> pdb=" O VAL D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 124 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.572A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.786A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY E 132 " --> pdb=" O ARG E 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.545A pdb=" N GLY F 28 " --> pdb=" O ASN F 25 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 25 through 29' Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 50 through 76 removed outlier: 3.955A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.517A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.530A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 98 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 removed outlier: 4.006A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 124 removed outlier: 3.640A pdb=" N ALA H 124 " --> pdb=" O LYS H 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 11 through 38 removed outlier: 3.697A pdb=" N LYS K 38 " --> pdb=" O ARG K 34 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 54 Processing helix chain 'K' and resid 54 through 76 removed outlier: 3.637A pdb=" N VAL K 58 " --> pdb=" O SER K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 99 Processing helix chain 'K' and resid 107 through 114 Processing helix chain 'K' and resid 146 through 158 Processing helix chain 'K' and resid 171 through 176 Processing helix chain 'K' and resid 250 through 261 Processing helix chain 'K' and resid 271 through 277 removed outlier: 3.782A pdb=" N TYR K 277 " --> pdb=" O VAL K 273 " (cutoff:3.500A) Processing helix chain 'K' and resid 301 through 307 removed outlier: 3.683A pdb=" N ASP K 305 " --> pdb=" O THR K 301 " (cutoff:3.500A) Processing helix chain 'K' and resid 314 through 327 Processing helix chain 'K' and resid 338 through 344 removed outlier: 4.510A pdb=" N SER K 342 " --> pdb=" O ASP K 338 " (cutoff:3.500A) Processing helix chain 'K' and resid 350 through 355 removed outlier: 3.877A pdb=" N SER K 354 " --> pdb=" O GLY K 350 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.700A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'K' and resid 183 through 185 removed outlier: 6.318A pdb=" N VAL K 164 " --> pdb=" O SER K 184 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N VAL K 103 " --> pdb=" O LEU K 265 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N LEU K 267 " --> pdb=" O VAL K 103 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N TYR K 105 " --> pdb=" O LEU K 267 " (cutoff:3.500A) removed outlier: 9.974A pdb=" N LEU K 311 " --> pdb=" O LEU K 293 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ILE K 295 " --> pdb=" O LEU K 311 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 192 through 194 498 hydrogen bonds defined for protein. 1482 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 339 hydrogen bonds 670 hydrogen bond angles 0 basepair planarities 136 basepair parallelities 251 stacking parallelities Total time for adding SS restraints: 5.63 Time building geometry restraints manager: 4.01 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 37.600 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.360 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.021 0.003 TRP K 281 HIS 0.007 0.001 HIS K 156 PHE 0.023 0.003 PHE D 65 TYR 0.041 0.002 TYR A 99 ARG 0.007 0.001 ARG A 131 Details of bonding type rmsd hydrogen bonds : bond 0.11633 ( 837) hydrogen bonds : angle 5.20619 ( 2152) covalent geometry : bond 0.00384 (15502) covalent geometry : angle 0.73928 (22197) *********************** 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 : 1.110 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: 0.3814 time to fit residues: 188.5737 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 : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 67 optimal weight: 0.0470 chunk 53 optimal weight: 2.9990 chunk 103 optimal weight: 40.0000 chunk 40 optimal weight: 0.0870 chunk 62 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN C 31 HIS ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN E 85 GLN F 93 GLN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS K 24 GLN ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.154489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.129839 restraints weight = 70878.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.131080 restraints weight = 35709.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.132144 restraints weight = 22971.689| |-----------------------------------------------------------------------------| r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15502 Z= 0.171 Angle : 0.655 13.931 22197 Z= 0.372 Chirality : 0.037 0.166 2514 Planarity : 0.006 0.060 1798 Dihedral : 29.676 174.260 4471 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.32 % Allowed : 13.95 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.25), residues: 1061 helix: 0.94 (0.20), residues: 670 sheet: 1.03 (0.87), residues: 42 loop : -0.14 (0.30), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 251 HIS 0.011 0.002 HIS H 109 PHE 0.025 0.002 PHE E 67 TYR 0.027 0.002 TYR B 88 ARG 0.026 0.001 ARG K 30 Details of bonding type rmsd hydrogen bonds : bond 0.05150 ( 837) hydrogen bonds : angle 3.78632 ( 2152) covalent geometry : bond 0.00372 (15502) covalent geometry : angle 0.65547 (22197) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 228 time to evaluate : 1.102 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: A 50 GLU cc_start: 0.8678 (tp30) cc_final: 0.7909 (tp30) REVERT: B 77 LYS cc_start: 0.8935 (mtpt) cc_final: 0.8540 (tptt) REVERT: C 25 PHE cc_start: 0.6917 (m-80) cc_final: 0.6620 (m-80) REVERT: C 94 ASN cc_start: 0.8582 (m-40) cc_final: 0.8300 (m-40) REVERT: D 108 LYS cc_start: 0.7254 (mttt) cc_final: 0.6676 (mmtt) REVERT: F 85 ASP cc_start: 0.8872 (m-30) cc_final: 0.8626 (m-30) REVERT: H 83 TYR cc_start: 0.7691 (m-10) cc_final: 0.7257 (m-10) REVERT: K 23 GLU cc_start: 0.8852 (tp30) cc_final: 0.8488 (tm-30) REVERT: K 47 GLU cc_start: 0.6164 (tm-30) cc_final: 0.5723 (pt0) REVERT: K 283 MET cc_start: 0.5617 (mmm) cc_final: 0.4927 (mmm) REVERT: K 319 MET cc_start: 0.8399 (mmm) cc_final: 0.7829 (mmt) outliers start: 30 outliers final: 15 residues processed: 246 average time/residue: 0.2955 time to fit residues: 100.5730 Evaluate side-chains 188 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 173 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain K residue 325 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 74 optimal weight: 20.0000 chunk 35 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 HIS ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN G 38 ASN H 49 HIS H 84 ASN K 25 GLN ** K 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.134543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.104357 restraints weight = 62585.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.106565 restraints weight = 31226.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.107784 restraints weight = 20510.933| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 15502 Z= 0.175 Angle : 0.619 7.671 22197 Z= 0.355 Chirality : 0.036 0.216 2514 Planarity : 0.005 0.047 1798 Dihedral : 29.622 174.328 4471 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 4.43 % Allowed : 17.83 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.25), residues: 1061 helix: 1.15 (0.20), residues: 670 sheet: 1.24 (0.89), residues: 42 loop : -0.10 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 251 HIS 0.010 0.002 HIS H 109 PHE 0.038 0.002 PHE D 65 TYR 0.014 0.002 TYR H 83 ARG 0.008 0.001 ARG F 39 Details of bonding type rmsd hydrogen bonds : bond 0.04807 ( 837) hydrogen bonds : angle 3.56206 ( 2152) covalent geometry : bond 0.00384 (15502) covalent geometry : angle 0.61893 (22197) *********************** 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 237 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 197 time to evaluate : 1.178 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: 0.8776 (tp30) cc_final: 0.7919 (tp30) REVERT: B 49 LEU cc_start: 0.8733 (mp) cc_final: 0.8516 (mp) REVERT: B 77 LYS cc_start: 0.8973 (mtpt) cc_final: 0.8468 (tptt) REVERT: C 85 LEU cc_start: 0.8801 (mt) cc_final: 0.8596 (mp) REVERT: C 94 ASN cc_start: 0.8642 (m-40) cc_final: 0.8019 (m-40) REVERT: D 63 ASN cc_start: 0.8565 (OUTLIER) cc_final: 0.7942 (t160) REVERT: D 84 ASN cc_start: 0.8524 (OUTLIER) cc_final: 0.8109 (m110) REVERT: D 108 LYS cc_start: 0.7403 (mttt) cc_final: 0.6774 (mmtt) REVERT: E 59 GLU cc_start: 0.7498 (pp20) cc_final: 0.6923 (pp20) REVERT: E 60 LEU cc_start: 0.7252 (mm) cc_final: 0.6692 (tp) REVERT: E 63 ARG cc_start: 0.6839 (mpt180) cc_final: 0.6399 (mmt90) REVERT: E 125 GLN cc_start: 0.8427 (mt0) cc_final: 0.8180 (mp10) REVERT: F 31 LYS cc_start: 0.9020 (tmtt) cc_final: 0.8528 (tptp) REVERT: F 84 MET cc_start: 0.8705 (tpp) cc_final: 0.8435 (tpp) REVERT: F 85 ASP cc_start: 0.9021 (m-30) cc_final: 0.8799 (m-30) REVERT: G 36 LYS cc_start: 0.8149 (mmtp) cc_final: 0.7836 (mmtm) REVERT: H 79 ARG cc_start: 0.8387 (ttm-80) cc_final: 0.7884 (ttm-80) REVERT: K 23 GLU cc_start: 0.8834 (tp30) cc_final: 0.8574 (tm-30) REVERT: K 47 GLU cc_start: 0.6618 (tm-30) cc_final: 0.5656 (pt0) REVERT: K 190 MET cc_start: 0.1422 (mmm) cc_final: 0.0898 (mmm) REVERT: K 283 MET cc_start: 0.5442 (mmm) cc_final: 0.4646 (mmm) REVERT: K 319 MET cc_start: 0.8335 (mmm) cc_final: 0.7855 (mmt) outliers start: 40 outliers final: 19 residues processed: 224 average time/residue: 0.2883 time to fit residues: 91.0091 Evaluate side-chains 189 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 168 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain D residue 99 ARG Chi-restraints excluded: chain E residue 54 TYR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 93 LEU 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 210 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 131 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 113 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 129 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN K 75 GLN ** K 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 312 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 = 0.4114 r_free = 0.4114 target = 0.110123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.075239 restraints weight = 54295.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.077191 restraints weight = 25963.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.078327 restraints weight = 17337.047| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.7278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.097 15502 Z= 0.412 Angle : 0.932 10.851 22197 Z= 0.525 Chirality : 0.051 0.215 2514 Planarity : 0.009 0.100 1798 Dihedral : 30.479 173.269 4471 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 25.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 6.87 % Allowed : 19.27 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.24), residues: 1061 helix: 0.18 (0.19), residues: 667 sheet: 0.77 (0.83), residues: 42 loop : -0.41 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K 306 HIS 0.010 0.003 HIS D 49 PHE 0.042 0.005 PHE D 65 TYR 0.042 0.004 TYR B 98 ARG 0.012 0.001 ARG F 39 Details of bonding type rmsd hydrogen bonds : bond 0.08970 ( 837) hydrogen bonds : angle 4.57267 ( 2152) covalent geometry : bond 0.00932 (15502) covalent geometry : angle 0.93189 (22197) *********************** 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 285 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 223 time to evaluate : 1.118 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: 0.8891 (tp30) cc_final: 0.7969 (tp30) REVERT: A 56 LYS cc_start: 0.8698 (tttp) cc_final: 0.8432 (tmtt) REVERT: B 77 LYS cc_start: 0.9352 (mtpt) cc_final: 0.8843 (tptt) REVERT: C 61 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8102 (mp0) REVERT: C 81 ARG cc_start: 0.7660 (tpm170) cc_final: 0.7362 (tpt170) REVERT: D 46 LYS cc_start: 0.8817 (ttpt) cc_final: 0.8370 (pttt) REVERT: D 82 HIS cc_start: 0.8929 (t70) cc_final: 0.8693 (t70) REVERT: D 108 LYS cc_start: 0.8220 (mttt) cc_final: 0.7571 (mmtm) REVERT: E 50 GLU cc_start: 0.8200 (pt0) cc_final: 0.7954 (pt0) REVERT: E 59 GLU cc_start: 0.8214 (pp20) cc_final: 0.7875 (pp20) REVERT: E 60 LEU cc_start: 0.8437 (mm) cc_final: 0.7932 (mt) REVERT: E 68 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.7662 (tp-100) REVERT: E 81 ASP cc_start: 0.8027 (m-30) cc_final: 0.7695 (t0) REVERT: E 125 GLN cc_start: 0.8353 (mt0) cc_final: 0.8062 (mp10) REVERT: F 31 LYS cc_start: 0.9180 (tmtt) cc_final: 0.8939 (tmtt) REVERT: F 63 GLU cc_start: 0.7915 (pp20) cc_final: 0.7648 (tm-30) REVERT: F 74 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8332 (tp30) REVERT: G 36 LYS cc_start: 0.9189 (mmtp) cc_final: 0.8917 (mmtm) REVERT: G 38 ASN cc_start: 0.8964 (p0) cc_final: 0.8742 (p0) REVERT: G 94 ASN cc_start: 0.9090 (t0) cc_final: 0.8833 (t0) REVERT: H 62 MET cc_start: 0.9283 (tpp) cc_final: 0.9057 (tpp) REVERT: H 93 GLU cc_start: 0.8303 (mp0) cc_final: 0.8002 (mp0) REVERT: K 23 GLU cc_start: 0.8945 (tp30) cc_final: 0.8669 (tm-30) REVERT: K 35 ILE cc_start: 0.7264 (tt) cc_final: 0.6984 (tt) REVERT: K 47 GLU cc_start: 0.6262 (tm-30) cc_final: 0.5453 (pt0) REVERT: K 150 MET cc_start: 0.5657 (mmp) cc_final: 0.5351 (mmp) REVERT: K 280 LEU cc_start: 0.8928 (mt) cc_final: 0.8520 (pp) REVERT: K 283 MET cc_start: 0.5881 (mmm) cc_final: 0.4639 (tpp) REVERT: K 319 MET cc_start: 0.8489 (mmm) cc_final: 0.7649 (mmt) outliers start: 62 outliers final: 33 residues processed: 261 average time/residue: 0.3106 time to fit residues: 111.3799 Evaluate side-chains 220 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 185 time to evaluate : 1.263 ------------------------------------------------------------------------------- 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 58 LEU Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 325 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 29 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 83 optimal weight: 9.9990 chunk 97 optimal weight: 8.9990 chunk 77 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 130 optimal weight: 7.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 HIS ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 ASN H 84 ASN ** K 173 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 = 0.4169 r_free = 0.4169 target = 0.114164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.079586 restraints weight = 53755.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.081696 restraints weight = 25001.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.082915 restraints weight = 16375.996| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.7249 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= 0.174 Angle : 0.669 12.832 22197 Z= 0.378 Chirality : 0.038 0.287 2514 Planarity : 0.005 0.043 1798 Dihedral : 30.337 173.116 4471 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.88 % Allowed : 26.47 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.25), residues: 1061 helix: 0.91 (0.20), residues: 673 sheet: 1.09 (0.85), residues: 42 loop : -0.37 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 251 HIS 0.006 0.001 HIS K 355 PHE 0.025 0.002 PHE D 65 TYR 0.054 0.003 TYR H 83 ARG 0.012 0.001 ARG G 71 Details of bonding type rmsd hydrogen bonds : bond 0.04911 ( 837) hydrogen bonds : angle 3.61163 ( 2152) covalent geometry : bond 0.00388 (15502) covalent geometry : angle 0.66933 (22197) *********************** 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 257 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 222 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8698 (tp30) cc_final: 0.8052 (tp30) REVERT: A 56 LYS cc_start: 0.8561 (tttp) cc_final: 0.8265 (tmtt) REVERT: A 106 ASP cc_start: 0.8617 (m-30) cc_final: 0.8347 (t0) REVERT: B 63 GLU cc_start: 0.8344 (pt0) cc_final: 0.7831 (pt0) REVERT: B 77 LYS cc_start: 0.9115 (mtpt) cc_final: 0.8610 (tptt) REVERT: C 57 TYR cc_start: 0.7986 (t80) cc_final: 0.7679 (t80) REVERT: C 81 ARG cc_start: 0.7564 (tpm170) cc_final: 0.7278 (tpt170) REVERT: C 104 GLN cc_start: 0.8246 (mp10) cc_final: 0.7889 (mm-40) REVERT: D 108 LYS cc_start: 0.8031 (mttt) cc_final: 0.7416 (mmtm) REVERT: E 59 GLU cc_start: 0.8159 (pp20) cc_final: 0.7794 (pp20) REVERT: E 60 LEU cc_start: 0.8467 (mm) cc_final: 0.7593 (mt) REVERT: E 68 GLN cc_start: 0.7906 (tp-100) cc_final: 0.7640 (tp40) REVERT: E 79 LYS cc_start: 0.8190 (ptmm) cc_final: 0.7937 (pttt) REVERT: E 125 GLN cc_start: 0.8333 (mt0) cc_final: 0.8016 (mp10) REVERT: F 31 LYS cc_start: 0.9229 (tmtt) cc_final: 0.8965 (tmtt) REVERT: F 84 MET cc_start: 0.8578 (tpp) cc_final: 0.8220 (tpp) REVERT: G 32 ARG cc_start: 0.8209 (ttp80) cc_final: 0.7854 (ttp-170) REVERT: G 38 ASN cc_start: 0.8941 (p0) cc_final: 0.8694 (p0) REVERT: G 41 GLU cc_start: 0.8149 (tt0) cc_final: 0.7744 (tp30) REVERT: G 51 MET cc_start: 0.8824 (mmt) cc_final: 0.8622 (mmm) REVERT: G 94 ASN cc_start: 0.9097 (t0) cc_final: 0.8839 (t0) REVERT: H 62 MET cc_start: 0.9187 (tpp) cc_final: 0.8897 (tpp) REVERT: H 93 GLU cc_start: 0.8012 (mp0) cc_final: 0.7708 (mp0) REVERT: K 35 ILE cc_start: 0.7253 (tt) cc_final: 0.6977 (tt) REVERT: K 47 GLU cc_start: 0.6491 (tm-30) cc_final: 0.5663 (pt0) REVERT: K 190 MET cc_start: 0.1864 (mmm) cc_final: 0.1448 (mmm) REVERT: K 283 MET cc_start: 0.5884 (mmm) cc_final: 0.4661 (tpp) REVERT: K 294 TYR cc_start: 0.8985 (OUTLIER) cc_final: 0.8725 (m-80) REVERT: K 319 MET cc_start: 0.8440 (mmm) cc_final: 0.7664 (mmt) outliers start: 35 outliers final: 20 residues processed: 243 average time/residue: 0.3022 time to fit residues: 103.5440 Evaluate side-chains 206 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 185 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 239 PHE Chi-restraints excluded: chain K residue 294 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 107 optimal weight: 10.0000 chunk 97 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 120 optimal weight: 10.0000 chunk 63 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 82 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 130 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- 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 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.111061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.075863 restraints weight = 53421.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.077895 restraints weight = 24769.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.079057 restraints weight = 16248.002| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.7660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 15502 Z= 0.230 Angle : 0.677 10.423 22197 Z= 0.384 Chirality : 0.039 0.213 2514 Planarity : 0.005 0.063 1798 Dihedral : 30.247 172.378 4471 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 5.09 % Allowed : 25.58 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.25), residues: 1061 helix: 1.02 (0.20), residues: 671 sheet: 1.19 (0.86), residues: 42 loop : -0.26 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K 300 HIS 0.009 0.002 HIS K 149 PHE 0.026 0.002 PHE D 65 TYR 0.077 0.003 TYR H 83 ARG 0.007 0.001 ARG F 95 Details of bonding type rmsd hydrogen bonds : bond 0.05349 ( 837) hydrogen bonds : angle 3.69644 ( 2152) covalent geometry : bond 0.00525 (15502) covalent geometry : angle 0.67662 (22197) *********************** 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 232 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 186 time to evaluate : 1.233 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: 0.8829 (tp30) cc_final: 0.8125 (tp30) REVERT: A 56 LYS cc_start: 0.8597 (tttp) cc_final: 0.8345 (tmtt) REVERT: A 106 ASP cc_start: 0.8685 (m-30) cc_final: 0.8472 (t0) REVERT: B 63 GLU cc_start: 0.8378 (pt0) cc_final: 0.7881 (pt0) REVERT: B 77 LYS cc_start: 0.9222 (mtpt) cc_final: 0.8739 (tptt) REVERT: C 61 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8234 (mp0) REVERT: C 81 ARG cc_start: 0.7699 (tpm170) cc_final: 0.7385 (tpt170) REVERT: C 104 GLN cc_start: 0.8415 (mp10) cc_final: 0.8039 (mm-40) REVERT: D 99 ARG cc_start: 0.8083 (ttm170) cc_final: 0.7785 (ttm170) REVERT: D 108 LYS cc_start: 0.8011 (mttt) cc_final: 0.7478 (mmtm) REVERT: E 50 GLU cc_start: 0.8275 (pt0) cc_final: 0.7869 (tt0) REVERT: E 59 GLU cc_start: 0.8071 (pp20) cc_final: 0.7736 (pp20) REVERT: E 60 LEU cc_start: 0.8388 (mm) cc_final: 0.7700 (mt) REVERT: E 79 LYS cc_start: 0.8326 (ptmm) cc_final: 0.8122 (pttt) REVERT: E 125 GLN cc_start: 0.8431 (mt0) cc_final: 0.8064 (mp10) REVERT: F 31 LYS cc_start: 0.9309 (tmtt) cc_final: 0.9098 (tttm) REVERT: F 40 ARG cc_start: 0.7338 (ttm170) cc_final: 0.6752 (tpp80) REVERT: F 63 GLU cc_start: 0.8511 (tp30) cc_final: 0.8226 (tp30) REVERT: F 84 MET cc_start: 0.8584 (tpp) cc_final: 0.8320 (tpp) REVERT: G 38 ASN cc_start: 0.9003 (p0) cc_final: 0.8580 (p0) REVERT: G 71 ARG cc_start: 0.8325 (mtm-85) cc_final: 0.7536 (mtm110) REVERT: G 94 ASN cc_start: 0.9124 (t0) cc_final: 0.8877 (t0) REVERT: H 62 MET cc_start: 0.9226 (tpp) cc_final: 0.8971 (tpp) REVERT: H 93 GLU cc_start: 0.8050 (mp0) cc_final: 0.7732 (mp0) REVERT: H 113 GLU cc_start: 0.8340 (tm-30) cc_final: 0.8132 (tm-30) REVERT: K 35 ILE cc_start: 0.7256 (tt) cc_final: 0.6968 (tt) REVERT: K 47 GLU cc_start: 0.6423 (tm-30) cc_final: 0.5646 (pt0) REVERT: K 150 MET cc_start: 0.5491 (mmp) cc_final: 0.5192 (mmp) REVERT: K 190 MET cc_start: 0.2192 (mmm) cc_final: 0.1771 (mmm) REVERT: K 265 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7327 (mt) REVERT: K 283 MET cc_start: 0.5971 (mmm) cc_final: 0.4526 (tmm) REVERT: K 293 LEU cc_start: 0.7044 (OUTLIER) cc_final: 0.6481 (mp) REVERT: K 294 TYR cc_start: 0.9016 (OUTLIER) cc_final: 0.8357 (m-80) REVERT: K 319 MET cc_start: 0.8471 (mmm) cc_final: 0.7780 (mmt) outliers start: 46 outliers final: 30 residues processed: 216 average time/residue: 0.2805 time to fit residues: 85.9286 Evaluate side-chains 215 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 181 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain K residue 207 VAL Chi-restraints excluded: chain K residue 210 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 Chi-restraints excluded: chain K residue 294 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 26 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 79 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 125 optimal weight: 6.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN ** K 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.112055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.077447 restraints weight = 53287.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.079507 restraints weight = 24425.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.080701 restraints weight = 15876.016| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.7911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 15502 Z= 0.176 Angle : 0.637 10.762 22197 Z= 0.361 Chirality : 0.037 0.206 2514 Planarity : 0.005 0.041 1798 Dihedral : 30.174 173.255 4471 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 4.65 % Allowed : 26.47 % Favored : 68.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.25), residues: 1061 helix: 1.20 (0.20), residues: 674 sheet: 1.44 (0.88), residues: 42 loop : -0.17 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K 251 HIS 0.007 0.001 HIS H 82 PHE 0.017 0.002 PHE E 67 TYR 0.070 0.002 TYR H 83 ARG 0.004 0.000 ARG F 95 Details of bonding type rmsd hydrogen bonds : bond 0.04556 ( 837) hydrogen bonds : angle 3.50024 ( 2152) covalent geometry : bond 0.00396 (15502) covalent geometry : angle 0.63712 (22197) *********************** 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 240 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 198 time to evaluate : 1.197 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: 0.8772 (tp30) cc_final: 0.8292 (tp30) REVERT: A 56 LYS cc_start: 0.8493 (tttp) cc_final: 0.8203 (tmtt) REVERT: B 63 GLU cc_start: 0.8268 (pt0) cc_final: 0.7803 (pt0) REVERT: B 77 LYS cc_start: 0.9182 (mtpt) cc_final: 0.8691 (tptt) REVERT: C 51 MET cc_start: 0.8306 (mmp) cc_final: 0.7814 (mmp) REVERT: C 57 TYR cc_start: 0.7976 (t80) cc_final: 0.7623 (t80) REVERT: C 81 ARG cc_start: 0.7572 (tpm170) cc_final: 0.7275 (tpt170) REVERT: C 104 GLN cc_start: 0.8395 (mp10) cc_final: 0.7964 (mm110) REVERT: D 62 MET cc_start: 0.8982 (mmp) cc_final: 0.8534 (mmm) REVERT: D 99 ARG cc_start: 0.8239 (ttm170) cc_final: 0.7965 (ttm170) REVERT: D 108 LYS cc_start: 0.7987 (mttt) cc_final: 0.7298 (mmtm) REVERT: E 59 GLU cc_start: 0.8084 (pp20) cc_final: 0.7848 (pp20) REVERT: E 60 LEU cc_start: 0.8430 (mm) cc_final: 0.7850 (mt) REVERT: E 125 GLN cc_start: 0.8446 (mt0) cc_final: 0.8050 (mp10) REVERT: F 31 LYS cc_start: 0.9328 (tmtt) cc_final: 0.9088 (tttm) REVERT: F 40 ARG cc_start: 0.7507 (ttm170) cc_final: 0.6751 (tpp80) REVERT: F 63 GLU cc_start: 0.8403 (tp30) cc_final: 0.8081 (tp30) REVERT: G 32 ARG cc_start: 0.8358 (tmm-80) cc_final: 0.7984 (tmm-80) REVERT: G 51 MET cc_start: 0.8881 (mmm) cc_final: 0.8614 (tpp) REVERT: G 71 ARG cc_start: 0.8262 (mtm-85) cc_final: 0.7508 (mtm110) REVERT: G 90 ASP cc_start: 0.8476 (t70) cc_final: 0.8210 (t0) REVERT: G 94 ASN cc_start: 0.9114 (t0) cc_final: 0.8898 (t0) REVERT: H 62 MET cc_start: 0.9202 (tpp) cc_final: 0.8957 (tpp) REVERT: H 93 GLU cc_start: 0.7943 (mp0) cc_final: 0.7479 (mt-10) REVERT: H 105 GLU cc_start: 0.7615 (tt0) cc_final: 0.7187 (tt0) REVERT: K 35 ILE cc_start: 0.7216 (tt) cc_final: 0.6932 (tt) REVERT: K 47 GLU cc_start: 0.6346 (tm-30) cc_final: 0.5576 (pt0) REVERT: K 150 MET cc_start: 0.5447 (mmp) cc_final: 0.5160 (mmp) REVERT: K 178 LEU cc_start: 0.5929 (mt) cc_final: 0.5532 (mt) REVERT: K 283 MET cc_start: 0.6128 (mmm) cc_final: 0.4672 (tmm) REVERT: K 294 TYR cc_start: 0.8958 (OUTLIER) cc_final: 0.8595 (m-80) REVERT: K 319 MET cc_start: 0.8446 (mmm) cc_final: 0.7760 (mmt) outliers start: 42 outliers final: 32 residues processed: 227 average time/residue: 0.2888 time to fit residues: 92.6458 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 : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 107 VAL 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 E residue 47 CYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain K residue 173 HIS Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 239 PHE Chi-restraints excluded: chain K residue 294 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 32 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 97 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 17 optimal weight: 0.2980 chunk 92 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN ** K 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.113828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.079779 restraints weight = 53080.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.081906 restraints weight = 24209.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 75)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.083112 restraints weight = 15615.150| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.7985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15502 Z= 0.155 Angle : 0.641 10.958 22197 Z= 0.358 Chirality : 0.036 0.304 2514 Planarity : 0.004 0.039 1798 Dihedral : 30.028 173.620 4471 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.32 % Allowed : 27.02 % Favored : 68.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.25), residues: 1061 helix: 1.22 (0.20), residues: 669 sheet: 1.38 (0.88), residues: 42 loop : -0.12 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 251 HIS 0.010 0.001 HIS H 82 PHE 0.017 0.001 PHE D 65 TYR 0.065 0.002 TYR H 83 ARG 0.009 0.000 ARG H 79 Details of bonding type rmsd hydrogen bonds : bond 0.04457 ( 837) hydrogen bonds : angle 3.44728 ( 2152) covalent geometry : bond 0.00338 (15502) covalent geometry : angle 0.64096 (22197) *********************** 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 237 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 198 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8740 (tp30) cc_final: 0.8242 (tp30) REVERT: A 56 LYS cc_start: 0.8479 (tttp) cc_final: 0.8170 (tmtt) REVERT: B 63 GLU cc_start: 0.8217 (pt0) cc_final: 0.7759 (pt0) REVERT: B 77 LYS cc_start: 0.9187 (mtpt) cc_final: 0.8696 (tptt) REVERT: B 88 TYR cc_start: 0.8462 (m-10) cc_final: 0.8249 (m-80) REVERT: C 51 MET cc_start: 0.8304 (mmp) cc_final: 0.7893 (mmp) REVERT: C 57 TYR cc_start: 0.7886 (t80) cc_final: 0.7494 (t80) REVERT: C 81 ARG cc_start: 0.7542 (tpm170) cc_final: 0.7252 (tpt170) REVERT: C 104 GLN cc_start: 0.8338 (mp10) cc_final: 0.7988 (mm110) REVERT: D 89 ILE cc_start: 0.8305 (OUTLIER) cc_final: 0.8031 (tt) REVERT: D 99 ARG cc_start: 0.8276 (ttm170) cc_final: 0.8061 (ttm170) REVERT: D 108 LYS cc_start: 0.7870 (mttt) cc_final: 0.7224 (mmtm) REVERT: E 59 GLU cc_start: 0.8082 (pp20) cc_final: 0.7824 (pp20) REVERT: E 60 LEU cc_start: 0.8336 (mm) cc_final: 0.7655 (mt) REVERT: E 77 ASP cc_start: 0.8355 (OUTLIER) cc_final: 0.8127 (p0) REVERT: E 125 GLN cc_start: 0.8481 (mt0) cc_final: 0.8048 (mp10) REVERT: F 31 LYS cc_start: 0.9314 (tmtt) cc_final: 0.9096 (tttm) REVERT: F 53 GLU cc_start: 0.8272 (tt0) cc_final: 0.8066 (tt0) REVERT: G 32 ARG cc_start: 0.8397 (tmm-80) cc_final: 0.7975 (tmm-80) REVERT: G 71 ARG cc_start: 0.8198 (mtm-85) cc_final: 0.7449 (mtm110) REVERT: G 94 ASN cc_start: 0.9076 (t0) cc_final: 0.8861 (t0) REVERT: H 39 ILE cc_start: 0.8969 (mm) cc_final: 0.8742 (mt) REVERT: H 93 GLU cc_start: 0.7795 (mp0) cc_final: 0.7415 (mt-10) REVERT: H 105 GLU cc_start: 0.7505 (tt0) cc_final: 0.7114 (tt0) REVERT: K 35 ILE cc_start: 0.7182 (tt) cc_final: 0.6907 (tt) REVERT: K 47 GLU cc_start: 0.6598 (tm-30) cc_final: 0.5961 (pt0) REVERT: K 150 MET cc_start: 0.5433 (mmp) cc_final: 0.5165 (mmp) REVERT: K 178 LEU cc_start: 0.5963 (mt) cc_final: 0.5725 (mt) REVERT: K 283 MET cc_start: 0.6032 (mmm) cc_final: 0.4559 (tmm) REVERT: K 319 MET cc_start: 0.8395 (mmm) cc_final: 0.7628 (mmt) outliers start: 39 outliers final: 26 residues processed: 224 average time/residue: 0.2919 time to fit residues: 92.3843 Evaluate side-chains 210 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 182 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 100 LEU 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 G residue 101 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 116 LYS 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 210 VAL Chi-restraints excluded: chain K residue 239 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 94 optimal weight: 1.9990 chunk 80 optimal weight: 0.4980 chunk 66 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 116 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 119 optimal weight: 10.0000 chunk 121 optimal weight: 8.9990 chunk 91 optimal weight: 30.0000 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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** ** K 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.112772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.078381 restraints weight = 53298.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.080423 restraints weight = 24323.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.081605 restraints weight = 15813.233| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.8157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 15502 Z= 0.173 Angle : 0.661 15.807 22197 Z= 0.366 Chirality : 0.037 0.272 2514 Planarity : 0.005 0.042 1798 Dihedral : 30.009 174.481 4471 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 4.10 % Allowed : 27.80 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.25), residues: 1061 helix: 1.12 (0.20), residues: 677 sheet: 1.49 (0.89), residues: 42 loop : -0.00 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 251 HIS 0.009 0.001 HIS H 82 PHE 0.014 0.002 PHE D 65 TYR 0.085 0.003 TYR H 83 ARG 0.006 0.001 ARG D 79 Details of bonding type rmsd hydrogen bonds : bond 0.04574 ( 837) hydrogen bonds : angle 3.55821 ( 2152) covalent geometry : bond 0.00389 (15502) covalent geometry : angle 0.66051 (22197) *********************** 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 236 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 199 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8807 (tp30) cc_final: 0.8309 (tp30) REVERT: A 56 LYS cc_start: 0.8526 (tttp) cc_final: 0.8231 (tmtt) REVERT: B 63 GLU cc_start: 0.8267 (pt0) cc_final: 0.7782 (pt0) REVERT: B 77 LYS cc_start: 0.9203 (mtpt) cc_final: 0.8714 (tptt) REVERT: C 23 LEU cc_start: 0.9066 (mm) cc_final: 0.8816 (mp) REVERT: C 51 MET cc_start: 0.8361 (mmp) cc_final: 0.7926 (mmp) REVERT: C 57 TYR cc_start: 0.7788 (t80) cc_final: 0.7395 (t80) REVERT: C 81 ARG cc_start: 0.7504 (tpm170) cc_final: 0.7226 (tpt170) REVERT: C 104 GLN cc_start: 0.8310 (mp10) cc_final: 0.7977 (mm110) REVERT: D 89 ILE cc_start: 0.8245 (OUTLIER) cc_final: 0.7998 (tt) REVERT: D 99 ARG cc_start: 0.8304 (ttm170) cc_final: 0.8079 (ttm170) REVERT: D 108 LYS cc_start: 0.7900 (mttt) cc_final: 0.7209 (mmtm) REVERT: E 59 GLU cc_start: 0.8089 (pp20) cc_final: 0.7832 (pp20) REVERT: E 60 LEU cc_start: 0.8275 (mm) cc_final: 0.7631 (mt) REVERT: E 77 ASP cc_start: 0.8316 (OUTLIER) cc_final: 0.8092 (p0) REVERT: E 125 GLN cc_start: 0.8513 (mt0) cc_final: 0.8079 (mp10) REVERT: F 31 LYS cc_start: 0.9308 (tmtt) cc_final: 0.9098 (tttm) REVERT: G 32 ARG cc_start: 0.8493 (tmm-80) cc_final: 0.8081 (tmm-80) REVERT: G 71 ARG cc_start: 0.8170 (mtm-85) cc_final: 0.7445 (mtm110) REVERT: G 90 ASP cc_start: 0.8459 (t70) cc_final: 0.8197 (t0) REVERT: G 94 ASN cc_start: 0.9116 (t0) cc_final: 0.8885 (t0) REVERT: H 93 GLU cc_start: 0.7938 (mp0) cc_final: 0.7505 (mt-10) REVERT: H 105 GLU cc_start: 0.7568 (tt0) cc_final: 0.7171 (tt0) REVERT: K 35 ILE cc_start: 0.7257 (tt) cc_final: 0.6963 (tt) REVERT: K 47 GLU cc_start: 0.6612 (tm-30) cc_final: 0.5951 (pt0) REVERT: K 150 MET cc_start: 0.5397 (mmp) cc_final: 0.5187 (mmp) REVERT: K 178 LEU cc_start: 0.5930 (mt) cc_final: 0.5493 (mt) REVERT: K 283 MET cc_start: 0.5945 (mmm) cc_final: 0.4526 (tmm) REVERT: K 319 MET cc_start: 0.8439 (mmm) cc_final: 0.7671 (mmt) outliers start: 37 outliers final: 28 residues processed: 225 average time/residue: 0.2865 time to fit residues: 91.4449 Evaluate side-chains 212 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 182 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 116 LYS 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 210 VAL Chi-restraints excluded: chain K residue 239 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 79 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 122 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 47 optimal weight: 0.1980 chunk 82 optimal weight: 0.0370 chunk 45 optimal weight: 0.0670 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN ** K 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.113934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.079675 restraints weight = 53986.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.081761 restraints weight = 24703.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.082971 restraints weight = 16069.312| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.8251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 15502 Z= 0.157 Angle : 0.665 12.151 22197 Z= 0.364 Chirality : 0.037 0.274 2514 Planarity : 0.004 0.042 1798 Dihedral : 29.923 174.974 4471 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.10 % Allowed : 29.46 % Favored : 67.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.26), residues: 1061 helix: 1.15 (0.20), residues: 666 sheet: 1.63 (0.92), residues: 42 loop : 0.10 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 251 HIS 0.006 0.001 HIS K 149 PHE 0.016 0.001 PHE D 65 TYR 0.074 0.003 TYR H 83 ARG 0.009 0.000 ARG E 52 Details of bonding type rmsd hydrogen bonds : bond 0.04413 ( 837) hydrogen bonds : angle 3.54647 ( 2152) covalent geometry : bond 0.00346 (15502) covalent geometry : angle 0.66498 (22197) ********************** 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 227 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 199 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8760 (tp30) cc_final: 0.8261 (tp30) REVERT: A 56 LYS cc_start: 0.8480 (tttp) cc_final: 0.8185 (tmtt) REVERT: A 90 MET cc_start: 0.8932 (mmp) cc_final: 0.8731 (mmp) REVERT: B 63 GLU cc_start: 0.8207 (pt0) cc_final: 0.7752 (pt0) REVERT: B 77 LYS cc_start: 0.9169 (mtpt) cc_final: 0.8673 (tptt) REVERT: C 23 LEU cc_start: 0.9021 (mm) cc_final: 0.8816 (mp) REVERT: C 57 TYR cc_start: 0.7790 (t80) cc_final: 0.7374 (t80) REVERT: C 81 ARG cc_start: 0.7413 (tpm170) cc_final: 0.7174 (tpt170) REVERT: C 104 GLN cc_start: 0.8273 (mp10) cc_final: 0.7967 (mm110) REVERT: D 59 MET cc_start: 0.9231 (tpp) cc_final: 0.8713 (tpt) REVERT: D 89 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.8016 (tt) REVERT: D 99 ARG cc_start: 0.7939 (ttm170) cc_final: 0.7663 (ttm170) REVERT: D 108 LYS cc_start: 0.7774 (mttt) cc_final: 0.7119 (mmtm) REVERT: E 59 GLU cc_start: 0.8029 (pp20) cc_final: 0.7815 (pp20) REVERT: E 60 LEU cc_start: 0.8355 (mm) cc_final: 0.7660 (mt) REVERT: E 125 GLN cc_start: 0.8559 (mt0) cc_final: 0.8213 (mp10) REVERT: F 31 LYS cc_start: 0.9292 (tmtt) cc_final: 0.9075 (tttm) REVERT: F 40 ARG cc_start: 0.7565 (ttm170) cc_final: 0.6563 (tpp80) REVERT: G 32 ARG cc_start: 0.8501 (tmm-80) cc_final: 0.8079 (tmm-80) REVERT: G 51 MET cc_start: 0.8814 (mmm) cc_final: 0.8612 (tpp) REVERT: G 71 ARG cc_start: 0.8174 (mtm-85) cc_final: 0.7461 (mtm110) REVERT: G 90 ASP cc_start: 0.8412 (t70) cc_final: 0.8154 (t0) REVERT: G 94 ASN cc_start: 0.9086 (t0) cc_final: 0.8868 (t0) REVERT: H 39 ILE cc_start: 0.8954 (mm) cc_final: 0.8734 (mt) REVERT: H 93 GLU cc_start: 0.7896 (mp0) cc_final: 0.7427 (mt-10) REVERT: H 105 GLU cc_start: 0.7539 (tt0) cc_final: 0.7184 (tt0) REVERT: K 47 GLU cc_start: 0.6629 (tm-30) cc_final: 0.5985 (pt0) REVERT: K 178 LEU cc_start: 0.5671 (mt) cc_final: 0.5282 (mt) REVERT: K 283 MET cc_start: 0.5946 (mmm) cc_final: 0.4508 (tmm) outliers start: 28 outliers final: 24 residues processed: 217 average time/residue: 0.2839 time to fit residues: 88.1437 Evaluate side-chains 211 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 186 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 116 LYS 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 210 VAL Chi-restraints excluded: chain K residue 239 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 85 optimal weight: 0.0980 chunk 99 optimal weight: 0.2980 chunk 56 optimal weight: 0.8980 chunk 105 optimal weight: 10.0000 chunk 74 optimal weight: 0.5980 chunk 73 optimal weight: 7.9990 chunk 84 optimal weight: 0.8980 chunk 98 optimal weight: 10.0000 chunk 82 optimal weight: 8.9990 chunk 80 optimal weight: 8.9990 chunk 110 optimal weight: 10.0000 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN ** K 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 158 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.114928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.080847 restraints weight = 53699.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.082899 restraints weight = 24620.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.084120 restraints weight = 16120.790| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.8332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15502 Z= 0.155 Angle : 0.672 12.128 22197 Z= 0.365 Chirality : 0.037 0.267 2514 Planarity : 0.004 0.045 1798 Dihedral : 29.848 175.769 4471 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.43 % Allowed : 29.24 % Favored : 67.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.26), residues: 1061 helix: 1.05 (0.20), residues: 667 sheet: 1.58 (0.91), residues: 42 loop : 0.15 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 251 HIS 0.013 0.001 HIS K 149 PHE 0.015 0.001 PHE D 65 TYR 0.052 0.002 TYR B 88 ARG 0.013 0.001 ARG C 35 Details of bonding type rmsd hydrogen bonds : bond 0.04419 ( 837) hydrogen bonds : angle 3.57033 ( 2152) covalent geometry : bond 0.00342 (15502) covalent geometry : angle 0.67208 (22197) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5773.24 seconds wall clock time: 100 minutes 53.59 seconds (6053.59 seconds total)