Starting phenix.real_space_refine on Thu Jun 12 22:03:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gmk_51449/06_2025/9gmk_51449.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gmk_51449/06_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_51449/06_2025/9gmk_51449.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gmk_51449/06_2025/9gmk_51449.map" model { file = "/net/cci-nas-00/data/ceres_data/9gmk_51449/06_2025/9gmk_51449.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gmk_51449/06_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-5710/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: 8.91, per 1000 atoms: 0.61 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: 3.75 Conformation dependent library (CDL) restraints added in 1.1 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: 6.36 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: 5.99 Time building geometry restraints manager: 4.45 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: 1.040 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: 0.600 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 38.760 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.060 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.640 ------------------------------------------------------------------------------- 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 : 1.494 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: 0.3908 time to fit residues: 194.2930 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 : 1.131 ------------------------------------------------------------------------------- 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 = 60)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.130281 restraints weight = 70878.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.131462 restraints weight = 36173.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.132478 restraints weight = 22884.503| |-----------------------------------------------------------------------------| r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 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 : 1.220 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: 0.8681 (tp30) cc_final: 0.7912 (tp30) REVERT: B 77 LYS cc_start: 0.8950 (mtpt) cc_final: 0.8541 (tptt) REVERT: C 25 PHE cc_start: 0.6918 (m-80) cc_final: 0.6618 (m-80) REVERT: C 94 ASN cc_start: 0.8578 (m-40) cc_final: 0.8296 (m-40) REVERT: D 108 LYS cc_start: 0.7274 (mttt) cc_final: 0.6688 (mmtt) REVERT: F 85 ASP cc_start: 0.8875 (m-30) cc_final: 0.8626 (m-30) REVERT: H 83 TYR cc_start: 0.7702 (m-10) cc_final: 0.7264 (m-10) REVERT: K 23 GLU cc_start: 0.8816 (tp30) cc_final: 0.8456 (tm-30) REVERT: K 47 GLU cc_start: 0.6292 (tm-30) cc_final: 0.5549 (pt0) REVERT: K 283 MET cc_start: 0.5574 (mmm) cc_final: 0.4831 (mmm) REVERT: K 319 MET cc_start: 0.8511 (mmm) cc_final: 0.7810 (mmt) outliers start: 30 outliers final: 15 residues processed: 246 average time/residue: 0.3125 time to fit residues: 106.8682 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 : 1.157 ------------------------------------------------------------------------------- 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 = 0.4428 r_free = 0.4428 target = 0.134615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.104454 restraints weight = 62613.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.106673 restraints weight = 31249.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.107928 restraints weight = 20470.301| |-----------------------------------------------------------------------------| r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15502 Z= 0.175 Angle : 0.621 7.616 22197 Z= 0.356 Chirality : 0.036 0.235 2514 Planarity : 0.005 0.047 1798 Dihedral : 29.622 174.331 4471 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 4.43 % Allowed : 17.61 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.04 (0.25), residues: 1061 helix: 1.14 (0.20), residues: 670 sheet: 1.23 (0.89), residues: 42 loop : -0.11 (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 0.034 0.002 PHE D 65 TYR 0.016 0.002 TYR B 88 ARG 0.007 0.001 ARG F 39 Details of bonding type rmsd hydrogen bonds : bond 0.04814 ( 837) hydrogen bonds : angle 3.57323 ( 2152) covalent geometry : bond 0.00385 (15502) covalent geometry : angle 0.62092 (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 235 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 195 time to evaluate : 1.199 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: 0.8771 (tp30) cc_final: 0.7916 (tp30) REVERT: B 49 LEU cc_start: 0.8731 (mp) cc_final: 0.8513 (mp) REVERT: B 77 LYS cc_start: 0.8983 (mtpt) cc_final: 0.8469 (tptt) REVERT: C 85 LEU cc_start: 0.8797 (mt) cc_final: 0.8593 (mp) REVERT: C 94 ASN cc_start: 0.8660 (m-40) cc_final: 0.8144 (m-40) REVERT: D 84 ASN cc_start: 0.8524 (OUTLIER) cc_final: 0.8109 (m110) REVERT: D 108 LYS cc_start: 0.7408 (mttt) cc_final: 0.6778 (mmtt) REVERT: E 59 GLU cc_start: 0.7498 (pp20) cc_final: 0.6922 (pp20) REVERT: E 60 LEU cc_start: 0.7250 (mm) cc_final: 0.6681 (tp) REVERT: E 63 ARG cc_start: 0.6827 (mpt180) cc_final: 0.6388 (mmt90) REVERT: E 125 GLN cc_start: 0.8425 (mt0) cc_final: 0.8185 (mp10) REVERT: F 31 LYS cc_start: 0.9018 (tmtt) cc_final: 0.8529 (tptp) REVERT: F 84 MET cc_start: 0.8696 (tpp) cc_final: 0.8431 (tpp) REVERT: F 85 ASP cc_start: 0.9020 (m-30) cc_final: 0.8793 (m-30) REVERT: G 36 LYS cc_start: 0.8137 (mmtp) cc_final: 0.7825 (mmtm) REVERT: H 79 ARG cc_start: 0.8388 (ttm-80) cc_final: 0.7885 (ttm-80) REVERT: K 23 GLU cc_start: 0.8825 (tp30) cc_final: 0.8564 (tm-30) REVERT: K 47 GLU cc_start: 0.6576 (tm-30) cc_final: 0.5588 (pt0) REVERT: K 190 MET cc_start: 0.1416 (mmm) cc_final: 0.0851 (mmm) REVERT: K 283 MET cc_start: 0.5466 (mmm) cc_final: 0.4669 (mmm) REVERT: K 319 MET cc_start: 0.8334 (mmm) cc_final: 0.7863 (mmt) outliers start: 40 outliers final: 19 residues processed: 222 average time/residue: 0.3376 time to fit residues: 108.2452 Evaluate side-chains 188 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 168 time to evaluate : 1.199 ------------------------------------------------------------------------------- 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 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: 9.9990 chunk 75 optimal weight: 10.0000 chunk 113 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 129 optimal weight: 6.9990 chunk 3 optimal weight: 0.4980 chunk 61 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 82 optimal weight: 8.9990 chunk 124 optimal weight: 6.9990 overall best weight: 4.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 ASN H 63 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.114463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.079829 restraints weight = 54004.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.081877 restraints weight = 25875.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.083048 restraints weight = 17199.096| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.6313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 15502 Z= 0.331 Angle : 0.799 9.264 22197 Z= 0.457 Chirality : 0.044 0.189 2514 Planarity : 0.007 0.078 1798 Dihedral : 30.139 173.336 4471 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 21.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 6.31 % Allowed : 19.60 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.39 (0.25), residues: 1061 helix: 0.59 (0.19), residues: 672 sheet: 1.08 (0.86), residues: 42 loop : -0.29 (0.31), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP K 251 HIS 0.008 0.002 HIS H 109 PHE 0.042 0.004 PHE D 65 TYR 0.033 0.004 TYR H 83 ARG 0.008 0.001 ARG F 67 Details of bonding type rmsd hydrogen bonds : bond 0.07006 ( 837) hydrogen bonds : angle 4.09031 ( 2152) covalent geometry : bond 0.00731 (15502) covalent geometry : angle 0.79935 (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 275 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 218 time to evaluate : 1.610 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: 0.8943 (tp30) cc_final: 0.8283 (tp30) REVERT: B 49 LEU cc_start: 0.8748 (mp) cc_final: 0.8418 (mp) REVERT: B 77 LYS cc_start: 0.9319 (mtpt) cc_final: 0.8825 (tptt) REVERT: C 57 TYR cc_start: 0.7697 (t80) cc_final: 0.7391 (t80) REVERT: D 68 ASP cc_start: 0.9145 (t0) cc_final: 0.8647 (t0) REVERT: D 99 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7799 (ttm170) REVERT: D 108 LYS cc_start: 0.8093 (mttt) cc_final: 0.7451 (mmtt) REVERT: E 50 GLU cc_start: 0.8208 (pt0) cc_final: 0.8001 (pt0) REVERT: E 53 ARG cc_start: 0.8579 (ptm160) cc_final: 0.8335 (ptp-170) REVERT: E 59 GLU cc_start: 0.8159 (pp20) cc_final: 0.7865 (pp20) REVERT: E 60 LEU cc_start: 0.8237 (mm) cc_final: 0.7419 (mt) REVERT: E 63 ARG cc_start: 0.7809 (mpt180) cc_final: 0.7584 (mmt180) REVERT: E 125 GLN cc_start: 0.8356 (mt0) cc_final: 0.8091 (mp10) REVERT: F 63 GLU cc_start: 0.7858 (pp20) cc_final: 0.7498 (tm-30) REVERT: F 67 ARG cc_start: 0.7280 (mtm110) cc_final: 0.6876 (ttp-110) REVERT: F 84 MET cc_start: 0.8487 (tpp) cc_final: 0.8145 (tpp) REVERT: G 36 LYS cc_start: 0.8984 (mmtp) cc_final: 0.8738 (mmtm) REVERT: G 38 ASN cc_start: 0.8862 (p0) cc_final: 0.8659 (p0) REVERT: G 74 LYS cc_start: 0.8684 (mmtt) cc_final: 0.8374 (pttt) REVERT: G 89 ASN cc_start: 0.8998 (OUTLIER) cc_final: 0.8777 (m110) REVERT: G 94 ASN cc_start: 0.9089 (t0) cc_final: 0.8866 (t0) REVERT: H 93 GLU cc_start: 0.7987 (mp0) cc_final: 0.7750 (mt-10) REVERT: K 23 GLU cc_start: 0.8916 (tp30) cc_final: 0.8576 (tm-30) REVERT: K 47 GLU cc_start: 0.6447 (tm-30) cc_final: 0.5546 (pt0) REVERT: K 150 MET cc_start: 0.5424 (mmp) cc_final: 0.5096 (mmp) REVERT: K 190 MET cc_start: 0.1790 (mmm) cc_final: 0.1319 (mmm) REVERT: K 283 MET cc_start: 0.5609 (mmm) cc_final: 0.4812 (mmm) REVERT: K 319 MET cc_start: 0.8507 (mmm) cc_final: 0.7801 (mmt) outliers start: 57 outliers final: 27 residues processed: 251 average time/residue: 0.4475 time to fit residues: 158.0062 Evaluate side-chains 207 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 178 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 134 ARG 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 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 99 ARG Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain G residue 100 VAL 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 K residue 78 VAL Chi-restraints excluded: chain K residue 192 ILE 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: 0.8980 chunk 50 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 83 optimal weight: 9.9990 chunk 97 optimal weight: 0.0970 chunk 77 optimal weight: 8.9990 chunk 43 optimal weight: 0.4980 chunk 11 optimal weight: 5.9990 chunk 130 optimal weight: 8.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 ASN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 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 = 0.4207 r_free = 0.4207 target = 0.117193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.082697 restraints weight = 52719.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.084860 restraints weight = 24613.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.086081 restraints weight = 15970.005| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.6377 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= 0.162 Angle : 0.646 14.336 22197 Z= 0.363 Chirality : 0.037 0.267 2514 Planarity : 0.005 0.039 1798 Dihedral : 30.045 173.400 4471 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.88 % Allowed : 24.25 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.93 (0.25), residues: 1061 helix: 1.06 (0.20), residues: 672 sheet: 1.21 (0.85), residues: 42 loop : -0.18 (0.31), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 300 HIS 0.006 0.001 HIS B 75 PHE 0.033 0.002 PHE D 65 TYR 0.036 0.002 TYR H 83 ARG 0.008 0.001 ARG G 71 Details of bonding type rmsd hydrogen bonds : bond 0.04619 ( 837) hydrogen bonds : angle 3.54639 ( 2152) covalent geometry : bond 0.00354 (15502) covalent geometry : angle 0.64635 (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 248 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 213 time to evaluate : 1.213 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: 0.8694 (tp30) cc_final: 0.8055 (tp30) REVERT: A 106 ASP cc_start: 0.8685 (m-30) cc_final: 0.8392 (t0) REVERT: B 88 TYR cc_start: 0.8498 (m-80) cc_final: 0.8249 (m-80) REVERT: C 81 ARG cc_start: 0.7381 (tpm170) cc_final: 0.7091 (tpt170) REVERT: C 94 ASN cc_start: 0.8783 (OUTLIER) cc_final: 0.8398 (t0) REVERT: D 42 TYR cc_start: 0.7950 (t80) cc_final: 0.7221 (t80) REVERT: D 46 LYS cc_start: 0.8595 (ttpt) cc_final: 0.8054 (pttt) REVERT: D 59 MET cc_start: 0.9157 (tpp) cc_final: 0.8466 (tpt) REVERT: D 108 LYS cc_start: 0.7799 (mttt) cc_final: 0.7162 (mmtm) REVERT: E 59 GLU cc_start: 0.8039 (pp20) cc_final: 0.7667 (pp20) REVERT: E 60 LEU cc_start: 0.7746 (mm) cc_final: 0.7258 (mt) REVERT: E 74 ILE cc_start: 0.9154 (tt) cc_final: 0.8890 (mt) REVERT: E 97 GLU cc_start: 0.7355 (pp20) cc_final: 0.7109 (pp20) REVERT: E 125 GLN cc_start: 0.8358 (mt0) cc_final: 0.8022 (mp10) REVERT: E 130 ILE cc_start: 0.9005 (mm) cc_final: 0.8784 (mm) REVERT: G 36 LYS cc_start: 0.8651 (mmtp) cc_final: 0.8369 (mmtm) REVERT: G 56 GLU cc_start: 0.8270 (tp30) cc_final: 0.7701 (tp30) REVERT: G 74 LYS cc_start: 0.8640 (mmtt) cc_final: 0.8433 (pttt) REVERT: G 94 ASN cc_start: 0.9034 (t0) cc_final: 0.8777 (t0) REVERT: H 93 GLU cc_start: 0.7879 (mp0) cc_final: 0.7565 (mp0) REVERT: K 47 GLU cc_start: 0.6439 (tm-30) cc_final: 0.5608 (pt0) REVERT: K 283 MET cc_start: 0.5631 (mmm) cc_final: 0.4177 (tmm) REVERT: K 294 TYR cc_start: 0.8951 (OUTLIER) cc_final: 0.8713 (m-80) REVERT: K 319 MET cc_start: 0.8438 (mmm) cc_final: 0.7727 (mmt) outliers start: 35 outliers final: 21 residues processed: 238 average time/residue: 0.3213 time to fit residues: 105.9155 Evaluate side-chains 202 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 179 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain G residue 100 VAL 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 K residue 11 ARG 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: 6.9990 chunk 41 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 130 optimal weight: 8.9990 chunk 43 optimal weight: 0.2980 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 ASN E 68 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 ASN H 84 ASN ** K 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.114263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.079372 restraints weight = 54014.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.081442 restraints weight = 25388.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.082634 restraints weight = 16659.643| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.6820 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= 0.220 Angle : 0.662 11.576 22197 Z= 0.374 Chirality : 0.038 0.240 2514 Planarity : 0.005 0.051 1798 Dihedral : 30.015 172.834 4471 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.43 % Allowed : 24.47 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.06 (0.25), residues: 1061 helix: 1.18 (0.20), residues: 672 sheet: 1.37 (0.86), residues: 42 loop : -0.18 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 251 HIS 0.006 0.001 HIS K 355 PHE 0.035 0.002 PHE D 65 TYR 0.074 0.003 TYR H 83 ARG 0.005 0.001 ARG F 67 Details of bonding type rmsd hydrogen bonds : bond 0.05070 ( 837) hydrogen bonds : angle 3.63068 ( 2152) covalent geometry : bond 0.00497 (15502) covalent geometry : angle 0.66211 (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 221 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 181 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8816 (tp30) cc_final: 0.8147 (tp30) REVERT: A 106 ASP cc_start: 0.8651 (m-30) cc_final: 0.8399 (t0) REVERT: B 63 GLU cc_start: 0.8378 (pt0) cc_final: 0.7867 (pt0) REVERT: C 81 ARG cc_start: 0.7421 (tpm170) cc_final: 0.7110 (tpt170) REVERT: D 108 LYS cc_start: 0.7936 (mttt) cc_final: 0.7325 (mmtm) REVERT: E 50 GLU cc_start: 0.8265 (pt0) cc_final: 0.7893 (tt0) REVERT: E 59 GLU cc_start: 0.8038 (pp20) cc_final: 0.7757 (pp20) REVERT: E 60 LEU cc_start: 0.7875 (mm) cc_final: 0.7294 (mt) REVERT: E 125 GLN cc_start: 0.8417 (mt0) cc_final: 0.8048 (mp10) REVERT: E 130 ILE cc_start: 0.9094 (mm) cc_final: 0.8877 (mm) REVERT: F 40 ARG cc_start: 0.7647 (ttp80) cc_final: 0.6847 (tpp80) REVERT: F 95 ARG cc_start: 0.8482 (mtt-85) cc_final: 0.8116 (ttm-80) REVERT: G 36 LYS cc_start: 0.8917 (mmtp) cc_final: 0.8671 (mmtm) REVERT: G 56 GLU cc_start: 0.8447 (tp30) cc_final: 0.7896 (tp30) REVERT: G 71 ARG cc_start: 0.8372 (mtt180) cc_final: 0.7767 (mtm110) REVERT: G 84 GLN cc_start: 0.9031 (OUTLIER) cc_final: 0.8802 (tp-100) REVERT: G 94 ASN cc_start: 0.9109 (t0) cc_final: 0.8856 (t0) REVERT: K 47 GLU cc_start: 0.6451 (tm-30) cc_final: 0.5630 (pt0) REVERT: K 265 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7585 (mm) REVERT: K 283 MET cc_start: 0.5739 (mmm) cc_final: 0.4538 (tpp) REVERT: K 292 LYS cc_start: 0.5963 (mmpt) cc_final: 0.5399 (ptpt) REVERT: K 293 LEU cc_start: 0.7167 (OUTLIER) cc_final: 0.6589 (mp) REVERT: K 294 TYR cc_start: 0.8982 (OUTLIER) cc_final: 0.8280 (m-80) REVERT: K 319 MET cc_start: 0.8465 (mmm) cc_final: 0.7796 (mmt) outliers start: 40 outliers final: 28 residues processed: 205 average time/residue: 0.3017 time to fit residues: 87.4463 Evaluate side-chains 199 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 167 time to evaluate : 1.342 ------------------------------------------------------------------------------- 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 64 LYS Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 84 GLN Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 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: 7.9990 chunk 91 optimal weight: 40.0000 chunk 54 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 95 optimal weight: 20.0000 chunk 57 optimal weight: 8.9990 chunk 125 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 HIS G 89 ASN ** K 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.108594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.073121 restraints weight = 53802.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.075071 restraints weight = 25170.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.076209 restraints weight = 16619.750| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.8114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 15502 Z= 0.306 Angle : 0.759 12.171 22197 Z= 0.428 Chirality : 0.043 0.231 2514 Planarity : 0.006 0.093 1798 Dihedral : 30.391 172.294 4471 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 18.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 6.09 % Allowed : 22.81 % Favored : 71.10 % 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: 0.82 (0.25), residues: 1061 helix: 0.96 (0.20), residues: 678 sheet: 0.91 (0.83), residues: 44 loop : -0.17 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 251 HIS 0.019 0.002 HIS H 82 PHE 0.033 0.003 PHE D 65 TYR 0.088 0.004 TYR H 83 ARG 0.008 0.001 ARG K 68 Details of bonding type rmsd hydrogen bonds : bond 0.06250 ( 837) hydrogen bonds : angle 4.00275 ( 2152) covalent geometry : bond 0.00694 (15502) covalent geometry : angle 0.75888 (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 247 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 192 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8924 (tp30) cc_final: 0.8225 (tp30) REVERT: A 56 LYS cc_start: 0.8653 (tttp) cc_final: 0.8376 (tmtt) REVERT: A 106 ASP cc_start: 0.8663 (m-30) cc_final: 0.8369 (t0) REVERT: B 63 GLU cc_start: 0.8511 (pt0) cc_final: 0.8017 (pt0) REVERT: C 57 TYR cc_start: 0.7986 (t80) cc_final: 0.7257 (t80) REVERT: C 81 ARG cc_start: 0.7684 (tpm170) cc_final: 0.7314 (tpt170) REVERT: D 99 ARG cc_start: 0.8637 (ttp80) cc_final: 0.8198 (ttm170) REVERT: D 108 LYS cc_start: 0.8175 (mttt) cc_final: 0.7519 (mmtm) REVERT: E 50 GLU cc_start: 0.8263 (pt0) cc_final: 0.7835 (tt0) REVERT: E 59 GLU cc_start: 0.8155 (pp20) cc_final: 0.7802 (pp20) REVERT: E 60 LEU cc_start: 0.8246 (mm) cc_final: 0.7689 (mt) REVERT: E 80 THR cc_start: 0.7587 (OUTLIER) cc_final: 0.7374 (t) REVERT: E 125 GLN cc_start: 0.8462 (mt0) cc_final: 0.8080 (mp10) REVERT: E 130 ILE cc_start: 0.9253 (mm) cc_final: 0.8849 (mm) REVERT: F 40 ARG cc_start: 0.7984 (ttp80) cc_final: 0.7144 (tpp80) REVERT: F 44 LYS cc_start: 0.8535 (mppt) cc_final: 0.8241 (tttm) REVERT: G 71 ARG cc_start: 0.8351 (mtt180) cc_final: 0.7660 (mtm110) REVERT: G 94 ASN cc_start: 0.9217 (t0) cc_final: 0.9010 (t0) REVERT: H 93 GLU cc_start: 0.8182 (mp0) cc_final: 0.7869 (mt-10) REVERT: H 105 GLU cc_start: 0.7875 (tt0) cc_final: 0.7325 (tt0) REVERT: K 47 GLU cc_start: 0.6297 (tm-30) cc_final: 0.5562 (pt0) REVERT: K 265 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7391 (mm) REVERT: K 283 MET cc_start: 0.6221 (mmm) cc_final: 0.5107 (tpp) REVERT: K 292 LYS cc_start: 0.5904 (mmpt) cc_final: 0.5329 (ptpt) REVERT: K 294 TYR cc_start: 0.8918 (OUTLIER) cc_final: 0.8383 (m-80) REVERT: K 319 MET cc_start: 0.8506 (mmm) cc_final: 0.7724 (mmt) outliers start: 55 outliers final: 43 residues processed: 224 average time/residue: 0.3043 time to fit residues: 96.5365 Evaluate side-chains 216 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 170 time to evaluate : 1.153 ------------------------------------------------------------------------------- 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 82 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 62 LEU 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 107 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 207 VAL Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 236 ILE Chi-restraints excluded: chain K residue 239 PHE Chi-restraints excluded: chain K residue 265 LEU 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: 0.8980 chunk 49 optimal weight: 1.9990 chunk 9 optimal weight: 0.0970 chunk 97 optimal weight: 8.9990 chunk 19 optimal weight: 0.0570 chunk 17 optimal weight: 4.9990 chunk 92 optimal weight: 30.0000 chunk 55 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.5496 ------------------------------------------------------------------------------- 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 G 89 ASN ** K 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.112423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.077754 restraints weight = 53568.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.079811 restraints weight = 24426.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.080988 restraints weight = 15912.950| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.8062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15502 Z= 0.160 Angle : 0.667 11.114 22197 Z= 0.371 Chirality : 0.038 0.339 2514 Planarity : 0.005 0.049 1798 Dihedral : 30.236 173.836 4471 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.43 % Allowed : 26.80 % Favored : 69.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.14 (0.25), residues: 1061 helix: 1.26 (0.20), residues: 672 sheet: 1.38 (0.87), residues: 42 loop : -0.19 (0.31), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 251 HIS 0.006 0.001 HIS K 355 PHE 0.035 0.002 PHE D 65 TYR 0.077 0.003 TYR H 83 ARG 0.011 0.001 ARG K 97 Details of bonding type rmsd hydrogen bonds : bond 0.04583 ( 837) hydrogen bonds : angle 3.54842 ( 2152) covalent geometry : bond 0.00350 (15502) covalent geometry : angle 0.66744 (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 231 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 200 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8695 (tp30) cc_final: 0.8012 (tp30) REVERT: A 56 LYS cc_start: 0.8520 (tttp) cc_final: 0.8235 (tmtt) REVERT: A 106 ASP cc_start: 0.8639 (m-30) cc_final: 0.8330 (t0) REVERT: B 63 GLU cc_start: 0.8241 (pt0) cc_final: 0.7753 (pt0) REVERT: C 57 TYR cc_start: 0.7863 (t80) cc_final: 0.7152 (t80) REVERT: C 81 ARG cc_start: 0.7500 (tpm170) cc_final: 0.7188 (tpt170) REVERT: D 99 ARG cc_start: 0.8427 (ttp80) cc_final: 0.7910 (ttm170) REVERT: D 108 LYS cc_start: 0.7880 (mttt) cc_final: 0.7177 (mmtm) REVERT: E 50 GLU cc_start: 0.8255 (pt0) cc_final: 0.7829 (tt0) REVERT: E 59 GLU cc_start: 0.8217 (pp20) cc_final: 0.7820 (pp20) REVERT: E 60 LEU cc_start: 0.8435 (mm) cc_final: 0.8027 (mt) REVERT: E 74 ILE cc_start: 0.9237 (tt) cc_final: 0.8978 (mt) REVERT: E 125 GLN cc_start: 0.8432 (mt0) cc_final: 0.8073 (mp10) REVERT: E 130 ILE cc_start: 0.9207 (mm) cc_final: 0.8962 (mm) REVERT: F 31 LYS cc_start: 0.9225 (tmtt) cc_final: 0.8995 (tttm) REVERT: F 40 ARG cc_start: 0.7767 (ttp80) cc_final: 0.6915 (tpp80) REVERT: G 56 GLU cc_start: 0.8418 (tp30) cc_final: 0.7891 (tt0) REVERT: G 71 ARG cc_start: 0.8123 (mtt180) cc_final: 0.7390 (mtm110) REVERT: G 91 GLU cc_start: 0.7564 (tm-30) cc_final: 0.7268 (tm-30) REVERT: H 93 GLU cc_start: 0.7872 (mp0) cc_final: 0.7487 (mt-10) REVERT: H 105 GLU cc_start: 0.7466 (tt0) cc_final: 0.6999 (tt0) REVERT: K 47 GLU cc_start: 0.6458 (tm-30) cc_final: 0.5720 (pt0) REVERT: K 265 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7449 (mm) REVERT: K 283 MET cc_start: 0.6039 (mmm) cc_final: 0.4593 (tmm) REVERT: K 292 LYS cc_start: 0.5818 (mmpt) cc_final: 0.5344 (ptpt) REVERT: K 294 TYR cc_start: 0.8933 (OUTLIER) cc_final: 0.8403 (m-80) REVERT: K 319 MET cc_start: 0.8513 (mmm) cc_final: 0.7735 (mmt) outliers start: 31 outliers final: 22 residues processed: 222 average time/residue: 0.3509 time to fit residues: 110.3933 Evaluate side-chains 207 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain C residue 58 LEU 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 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 E residue 100 LEU Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain K residue 11 ARG 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 294 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 94 optimal weight: 10.0000 chunk 80 optimal weight: 8.9990 chunk 66 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 116 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 121 optimal weight: 8.9990 chunk 91 optimal weight: 0.0170 overall best weight: 1.3620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 HIS ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN G 89 ASN ** K 24 GLN ** 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 = 0.4135 r_free = 0.4135 target = 0.112024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.076930 restraints weight = 53236.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.079010 restraints weight = 24344.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.080184 restraints weight = 15855.369| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.8192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15502 Z= 0.176 Angle : 0.670 10.938 22197 Z= 0.372 Chirality : 0.037 0.269 2514 Planarity : 0.005 0.041 1798 Dihedral : 30.121 173.185 4471 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.77 % Allowed : 27.80 % Favored : 69.44 % 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: 1.19 (0.25), residues: 1061 helix: 1.23 (0.20), residues: 678 sheet: 1.40 (0.88), residues: 42 loop : -0.04 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 251 HIS 0.006 0.001 HIS K 355 PHE 0.034 0.002 PHE D 65 TYR 0.071 0.003 TYR H 83 ARG 0.010 0.001 ARG G 32 Details of bonding type rmsd hydrogen bonds : bond 0.04620 ( 837) hydrogen bonds : angle 3.61163 ( 2152) covalent geometry : bond 0.00394 (15502) covalent geometry : angle 0.66982 (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 224 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 199 time to evaluate : 1.911 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: 0.8781 (tp30) cc_final: 0.8083 (tp30) REVERT: A 56 LYS cc_start: 0.8585 (tttp) cc_final: 0.8276 (tmtt) REVERT: A 106 ASP cc_start: 0.8607 (m-30) cc_final: 0.8383 (t0) REVERT: B 58 LEU cc_start: 0.9278 (tp) cc_final: 0.9075 (tt) REVERT: B 63 GLU cc_start: 0.8274 (pt0) cc_final: 0.7799 (pt0) REVERT: B 77 LYS cc_start: 0.8610 (mmtm) cc_final: 0.8401 (mmtt) REVERT: C 57 TYR cc_start: 0.7924 (t80) cc_final: 0.7199 (t80) REVERT: D 99 ARG cc_start: 0.8493 (ttp80) cc_final: 0.7944 (ttm170) REVERT: D 108 LYS cc_start: 0.7951 (mttt) cc_final: 0.7218 (mmtm) REVERT: E 50 GLU cc_start: 0.8259 (pt0) cc_final: 0.7832 (tt0) REVERT: E 59 GLU cc_start: 0.8226 (pp20) cc_final: 0.7845 (pp20) REVERT: E 60 LEU cc_start: 0.8503 (mm) cc_final: 0.8029 (mt) REVERT: E 125 GLN cc_start: 0.8515 (mt0) cc_final: 0.8195 (mp10) REVERT: F 31 LYS cc_start: 0.9234 (tmtt) cc_final: 0.9009 (tttm) REVERT: F 40 ARG cc_start: 0.7902 (ttp80) cc_final: 0.7028 (tpp80) REVERT: F 84 MET cc_start: 0.8440 (tpp) cc_final: 0.8172 (tpp) REVERT: G 56 GLU cc_start: 0.8423 (tp30) cc_final: 0.7885 (tt0) REVERT: G 71 ARG cc_start: 0.8128 (mtt180) cc_final: 0.7385 (mtm110) REVERT: G 90 ASP cc_start: 0.8422 (t0) cc_final: 0.8197 (t0) REVERT: H 93 GLU cc_start: 0.8000 (mp0) cc_final: 0.7623 (mt-10) REVERT: H 105 GLU cc_start: 0.7543 (tt0) cc_final: 0.7087 (tt0) REVERT: K 47 GLU cc_start: 0.6468 (tm-30) cc_final: 0.5744 (pt0) REVERT: K 236 ILE cc_start: 0.1865 (tp) cc_final: 0.1405 (pt) REVERT: K 265 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7447 (mm) REVERT: K 283 MET cc_start: 0.6083 (mmm) cc_final: 0.4634 (tmm) REVERT: K 292 LYS cc_start: 0.5852 (mmpt) cc_final: 0.5386 (ptpt) REVERT: K 294 TYR cc_start: 0.8971 (OUTLIER) cc_final: 0.8411 (m-80) outliers start: 25 outliers final: 19 residues processed: 214 average time/residue: 0.3511 time to fit residues: 107.9667 Evaluate side-chains 213 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 192 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 58 LEU 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 E residue 65 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain K residue 11 ARG 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 294 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 79 optimal weight: 9.9990 chunk 57 optimal weight: 0.8980 chunk 71 optimal weight: 7.9990 chunk 98 optimal weight: 0.9990 chunk 4 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 122 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 82 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.111180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.076017 restraints weight = 53266.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.078009 restraints weight = 24450.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.079189 restraints weight = 16050.382| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.8403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15502 Z= 0.194 Angle : 0.687 10.777 22197 Z= 0.380 Chirality : 0.038 0.261 2514 Planarity : 0.005 0.044 1798 Dihedral : 30.096 173.373 4471 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.99 % Allowed : 27.46 % Favored : 69.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.13 (0.25), residues: 1061 helix: 1.18 (0.20), residues: 678 sheet: 1.38 (0.89), residues: 42 loop : -0.04 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 251 HIS 0.008 0.001 HIS K 355 PHE 0.032 0.002 PHE D 65 TYR 0.061 0.003 TYR B 88 ARG 0.010 0.001 ARG G 32 Details of bonding type rmsd hydrogen bonds : bond 0.04712 ( 837) hydrogen bonds : angle 3.71743 ( 2152) covalent geometry : bond 0.00439 (15502) covalent geometry : angle 0.68747 (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 213 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 186 time to evaluate : 1.138 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: 0.8815 (tp30) cc_final: 0.8128 (tp30) REVERT: A 56 LYS cc_start: 0.8591 (tttp) cc_final: 0.8276 (tmtt) REVERT: A 106 ASP cc_start: 0.8584 (m-30) cc_final: 0.8351 (t0) REVERT: B 63 GLU cc_start: 0.8300 (pt0) cc_final: 0.7825 (pt0) REVERT: B 77 LYS cc_start: 0.8623 (mmtm) cc_final: 0.8415 (mmtt) REVERT: C 57 TYR cc_start: 0.7954 (t80) cc_final: 0.7180 (t80) REVERT: D 99 ARG cc_start: 0.8613 (ttp80) cc_final: 0.8095 (ttm170) REVERT: D 108 LYS cc_start: 0.7938 (mttt) cc_final: 0.7224 (mmtm) REVERT: E 50 GLU cc_start: 0.8221 (pt0) cc_final: 0.7820 (tt0) REVERT: E 59 GLU cc_start: 0.8258 (pp20) cc_final: 0.7867 (pp20) REVERT: E 60 LEU cc_start: 0.8563 (mm) cc_final: 0.8133 (mt) REVERT: E 125 GLN cc_start: 0.8527 (mt0) cc_final: 0.8204 (mp10) REVERT: F 31 LYS cc_start: 0.9225 (tmtt) cc_final: 0.9010 (tttm) REVERT: F 40 ARG cc_start: 0.7965 (ttp80) cc_final: 0.7078 (tpp80) REVERT: F 84 MET cc_start: 0.8381 (tpp) cc_final: 0.8155 (tpp) REVERT: G 20 ARG cc_start: 0.8645 (ttm170) cc_final: 0.8159 (ttm170) REVERT: G 56 GLU cc_start: 0.8454 (tp30) cc_final: 0.7886 (tt0) REVERT: G 71 ARG cc_start: 0.8188 (mtt180) cc_final: 0.7388 (mtm110) REVERT: H 93 GLU cc_start: 0.8014 (mp0) cc_final: 0.7670 (mp0) REVERT: H 105 GLU cc_start: 0.7649 (tt0) cc_final: 0.7150 (tt0) REVERT: K 47 GLU cc_start: 0.6447 (tm-30) cc_final: 0.5736 (pt0) REVERT: K 150 MET cc_start: 0.5923 (mmm) cc_final: 0.4828 (mpp) REVERT: K 265 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7472 (mm) REVERT: K 283 MET cc_start: 0.6027 (mmm) cc_final: 0.4598 (tmm) REVERT: K 292 LYS cc_start: 0.5918 (mmpt) cc_final: 0.5516 (ptpt) REVERT: K 294 TYR cc_start: 0.8873 (OUTLIER) cc_final: 0.8253 (m-80) outliers start: 27 outliers final: 21 residues processed: 204 average time/residue: 0.2942 time to fit residues: 85.9236 Evaluate side-chains 205 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 182 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 58 LEU 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 E residue 65 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 207 VAL Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 239 PHE Chi-restraints excluded: chain K residue 265 LEU Chi-restraints excluded: chain K residue 294 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 85 optimal weight: 40.0000 chunk 99 optimal weight: 20.0000 chunk 56 optimal weight: 0.0970 chunk 105 optimal weight: 10.0000 chunk 74 optimal weight: 0.0000 chunk 73 optimal weight: 1.9990 chunk 84 optimal weight: 30.0000 chunk 98 optimal weight: 8.9990 chunk 82 optimal weight: 5.9990 chunk 80 optimal weight: 9.9990 chunk 110 optimal weight: 8.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 HIS ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 ASN ** K 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 231 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.108154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.072671 restraints weight = 54475.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.074595 restraints weight = 25293.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.075700 restraints weight = 16829.993| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.8977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 15502 Z= 0.261 Angle : 0.743 11.672 22197 Z= 0.412 Chirality : 0.042 0.270 2514 Planarity : 0.005 0.045 1798 Dihedral : 30.279 172.462 4471 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 18.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.88 % Allowed : 26.36 % Favored : 69.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.95 (0.25), residues: 1061 helix: 0.99 (0.20), residues: 670 sheet: 1.28 (0.88), residues: 42 loop : 0.03 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 251 HIS 0.015 0.002 HIS K 173 PHE 0.032 0.002 PHE D 65 TYR 0.071 0.003 TYR B 88 ARG 0.009 0.001 ARG K 175 Details of bonding type rmsd hydrogen bonds : bond 0.05608 ( 837) hydrogen bonds : angle 3.95081 ( 2152) covalent geometry : bond 0.00589 (15502) covalent geometry : angle 0.74257 (22197) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6477.51 seconds wall clock time: 114 minutes 27.10 seconds (6867.10 seconds total)