Starting phenix.real_space_refine on Thu Mar 6 08:22:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t05_40935/03_2025/8t05_40935.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t05_40935/03_2025/8t05_40935.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t05_40935/03_2025/8t05_40935.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t05_40935/03_2025/8t05_40935.map" model { file = "/net/cci-nas-00/data/ceres_data/8t05_40935/03_2025/8t05_40935.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t05_40935/03_2025/8t05_40935.cif" } resolution = 3.22 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= 0.004 sd= 0.066 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 2 5.49 5 S 22 5.16 5 C 3387 2.51 5 N 798 2.21 5 O 893 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 5104 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1592 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 7, 'TRANS': 193} Chain: "B" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1592 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 7, 'TRANS': 193} Chain: "C" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "D" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "A" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 72 Unusual residues: {' ZN': 1, 'CLR': 1, 'LBN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'LBN:plan-3': 1} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 72 Unusual residues: {' ZN': 1, 'CLR': 1, 'LBN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'LBN:plan-3': 1} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 3.95, per 1000 atoms: 0.77 Number of scatterers: 5104 At special positions: 0 Unit cell: (81.34, 88.81, 113.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 22 16.00 P 2 15.00 O 893 8.00 N 798 7.00 C 3387 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 60 " distance=2.04 Simple disulfide: pdb=" SG CYS B 50 " - pdb=" SG CYS B 60 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.02 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.30 Conformation dependent library (CDL) restraints added in 620.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 182 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 186 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 48 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 48 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 186 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 182 " 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1158 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 4 sheets defined 55.6% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 2 through 14 removed outlier: 3.844A pdb=" N VAL A 6 " --> pdb=" O GLY A 2 " (cutoff:3.500A) Proline residue: A 11 - end of helix Processing helix chain 'A' and resid 15 through 17 No H-bonds generated for 'chain 'A' and resid 15 through 17' Processing helix chain 'A' and resid 18 through 28 removed outlier: 3.546A pdb=" N GLY A 22 " --> pdb=" O PHE A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 51 removed outlier: 4.083A pdb=" N LEU A 36 " --> pdb=" O THR A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 63 removed outlier: 3.692A pdb=" N MET A 62 " --> pdb=" O LEU A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 86 removed outlier: 3.738A pdb=" N THR A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 112 removed outlier: 3.555A pdb=" N GLU A 112 " --> pdb=" O ARG A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 142 Processing helix chain 'A' and resid 147 through 154 Processing helix chain 'A' and resid 154 through 171 Processing helix chain 'A' and resid 177 through 198 removed outlier: 3.787A pdb=" N SER A 183 " --> pdb=" O ALA A 179 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG A 198 " --> pdb=" O THR A 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 14 Proline residue: B 11 - end of helix Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 18 through 28 removed outlier: 3.721A pdb=" N GLY B 22 " --> pdb=" O PHE B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 52 Processing helix chain 'B' and resid 63 through 86 removed outlier: 3.628A pdb=" N PHE B 69 " --> pdb=" O LYS B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 112 Processing helix chain 'B' and resid 119 through 141 Processing helix chain 'B' and resid 147 through 153 Processing helix chain 'B' and resid 154 through 171 Processing helix chain 'B' and resid 177 through 197 removed outlier: 3.965A pdb=" N SER B 183 " --> pdb=" O ALA B 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.885A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'C' and resid 4 through 5 Processing sheet with id=AA2, first strand: chain 'C' and resid 10 through 11 removed outlier: 5.688A pdb=" N GLU C 10 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA C 92 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N MET C 34 " --> pdb=" O ALA C 50 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ALA C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.072A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 19 through 24 removed outlier: 3.533A pdb=" N VAL D 19 " --> pdb=" O ILE D 75 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) 298 hydrogen bonds defined for protein. 864 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.37 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 746 1.31 - 1.44: 1499 1.44 - 1.56: 2946 1.56 - 1.69: 14 1.69 - 1.82: 32 Bond restraints: 5237 Sorted by residual: bond pdb=" C GLY C 8 " pdb=" N ALA C 9 " ideal model delta sigma weight residual 1.331 1.409 -0.077 1.30e-02 5.92e+03 3.53e+01 bond pdb=" C25 LBN A 303 " pdb=" O5 LBN A 303 " ideal model delta sigma weight residual 1.326 1.433 -0.107 2.00e-02 2.50e+03 2.85e+01 bond pdb=" C25 LBN B 303 " pdb=" O5 LBN B 303 " ideal model delta sigma weight residual 1.326 1.429 -0.103 2.00e-02 2.50e+03 2.65e+01 bond pdb=" C34 LBN A 303 " pdb=" O7 LBN A 303 " ideal model delta sigma weight residual 1.331 1.427 -0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" C34 LBN B 303 " pdb=" O7 LBN B 303 " ideal model delta sigma weight residual 1.331 1.424 -0.093 2.00e-02 2.50e+03 2.16e+01 ... (remaining 5232 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.92: 6281 2.92 - 5.84: 805 5.84 - 8.76: 12 8.76 - 11.68: 5 11.68 - 14.60: 2 Bond angle restraints: 7105 Sorted by residual: angle pdb=" N PHE C 109 " pdb=" CA PHE C 109 " pdb=" C PHE C 109 " ideal model delta sigma weight residual 111.24 118.85 -7.61 1.38e+00 5.25e-01 3.04e+01 angle pdb=" C GLY A 101 " pdb=" N GLY A 102 " pdb=" CA GLY A 102 " ideal model delta sigma weight residual 120.03 125.59 -5.56 1.12e+00 7.97e-01 2.47e+01 angle pdb=" N THR D 94 " pdb=" CA THR D 94 " pdb=" C THR D 94 " ideal model delta sigma weight residual 108.82 117.00 -8.18 1.65e+00 3.67e-01 2.46e+01 angle pdb=" O1 LBN B 303 " pdb=" P1 LBN B 303 " pdb=" O2 LBN B 303 " ideal model delta sigma weight residual 93.45 108.05 -14.60 3.00e+00 1.11e-01 2.37e+01 angle pdb=" O1 LBN A 303 " pdb=" P1 LBN A 303 " pdb=" O2 LBN A 303 " ideal model delta sigma weight residual 93.45 107.88 -14.43 3.00e+00 1.11e-01 2.31e+01 ... (remaining 7100 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.48: 3038 30.48 - 60.96: 92 60.96 - 91.44: 11 91.44 - 121.92: 7 121.92 - 152.40: 4 Dihedral angle restraints: 3152 sinusoidal: 1337 harmonic: 1815 Sorted by residual: dihedral pdb=" CA THR D 94 " pdb=" C THR D 94 " pdb=" N PRO D 95 " pdb=" CA PRO D 95 " ideal model delta harmonic sigma weight residual 180.00 70.79 109.21 0 5.00e+00 4.00e-02 4.77e+02 dihedral pdb=" CA ALA D 50 " pdb=" C ALA D 50 " pdb=" N ALA D 51 " pdb=" CA ALA D 51 " ideal model delta harmonic sigma weight residual -180.00 -151.52 -28.48 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA SER B 56 " pdb=" C SER B 56 " pdb=" N LEU B 57 " pdb=" CA LEU B 57 " ideal model delta harmonic sigma weight residual -180.00 -155.12 -24.88 0 5.00e+00 4.00e-02 2.48e+01 ... (remaining 3149 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.985: 803 0.985 - 1.969: 0 1.969 - 2.954: 0 2.954 - 3.938: 0 3.938 - 4.923: 2 Chirality restraints: 805 Sorted by residual: chirality pdb=" C2 LBN B 303 " pdb=" C1 LBN B 303 " pdb=" C3 LBN B 303 " pdb=" O7 LBN B 303 " both_signs ideal model delta sigma weight residual False -2.36 2.56 -4.92 2.00e-01 2.50e+01 6.06e+02 chirality pdb=" C2 LBN A 303 " pdb=" C1 LBN A 303 " pdb=" C3 LBN A 303 " pdb=" O7 LBN A 303 " both_signs ideal model delta sigma weight residual False -2.36 2.55 -4.92 2.00e-01 2.50e+01 6.04e+02 chirality pdb=" C14 CLR A 302 " pdb=" C13 CLR A 302 " pdb=" C15 CLR A 302 " pdb=" C8 CLR A 302 " both_signs ideal model delta sigma weight residual False -2.32 -2.72 0.40 2.00e-01 2.50e+01 3.97e+00 ... (remaining 802 not shown) Planarity restraints: 848 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 145 " -0.060 5.00e-02 4.00e+02 9.05e-02 1.31e+01 pdb=" N PRO B 146 " 0.157 5.00e-02 4.00e+02 pdb=" CA PRO B 146 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 146 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 13 " -0.054 5.00e-02 4.00e+02 8.29e-02 1.10e+01 pdb=" N PRO C 14 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO C 14 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 14 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 94 " -0.042 5.00e-02 4.00e+02 6.45e-02 6.65e+00 pdb=" N PRO D 95 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO D 95 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 95 " -0.036 5.00e-02 4.00e+02 ... (remaining 845 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 71 2.68 - 3.23: 4609 3.23 - 3.79: 7701 3.79 - 4.34: 10686 4.34 - 4.90: 18018 Nonbonded interactions: 41085 Sorted by model distance: nonbonded pdb=" OE1 GLN A 44 " pdb="ZN ZN A 301 " model vdw 2.120 2.230 nonbonded pdb=" OE1 GLN B 44 " pdb="ZN ZN B 301 " model vdw 2.172 2.230 nonbonded pdb=" NH2 ARG D 61 " pdb=" OE2 GLU D 81 " model vdw 2.356 3.120 nonbonded pdb=" NH2 ARG A 108 " pdb=" O PRO A 116 " model vdw 2.413 3.120 nonbonded pdb=" O HIS D 90 " pdb=" ND1 HIS D 90 " model vdw 2.433 3.120 ... (remaining 41080 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 'B' } 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 individual isotropic 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: 1.250 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 18.030 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 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 : 0.014 0.107 5237 Z= 0.930 Angle : 1.851 14.605 7105 Z= 1.350 Chirality : 0.259 4.923 805 Planarity : 0.006 0.091 848 Dihedral : 16.958 152.400 1982 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.78 % Favored : 93.90 % Rotamer: Outliers : 0.93 % Allowed : 6.16 % Favored : 92.91 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: -2.10 (0.31), residues: 623 helix: -1.21 (0.25), residues: 313 sheet: -1.44 (0.49), residues: 86 loop : -1.32 (0.44), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 151 HIS 0.007 0.002 HIS D 90 PHE 0.019 0.002 PHE B 43 TYR 0.043 0.003 TYR D 49 ARG 0.003 0.000 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.523 Fit side-chains REVERT: A 137 GLU cc_start: 0.6864 (tp30) cc_final: 0.6262 (mm-30) REVERT: A 198 ARG cc_start: 0.6886 (ttm170) cc_final: 0.6588 (ttp80) REVERT: B 62 MET cc_start: 0.6309 (mtt) cc_final: 0.6034 (mtm) REVERT: B 184 ILE cc_start: 0.7178 (mm) cc_final: 0.6907 (mt) REVERT: C 10 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7500 (mp0) REVERT: C 28 THR cc_start: 0.8525 (m) cc_final: 0.8298 (t) REVERT: C 32 TYR cc_start: 0.8080 (m-80) cc_final: 0.7604 (m-80) REVERT: C 34 MET cc_start: 0.8066 (mmm) cc_final: 0.7480 (tpt) REVERT: D 30 TYR cc_start: 0.8035 (m-80) cc_final: 0.7673 (m-80) REVERT: D 71 TYR cc_start: 0.7538 (m-80) cc_final: 0.7100 (m-80) REVERT: D 100 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7906 (tp30) outliers start: 5 outliers final: 4 residues processed: 92 average time/residue: 0.2236 time to fit residues: 25.1982 Evaluate side-chains 79 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 PRO Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain D residue 90 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.0170 chunk 48 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN A 95 HIS B 113 ASN B 186 HIS D 6 GLN D 28 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.173021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.141092 restraints weight = 5944.509| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 2.19 r_work: 0.3623 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5237 Z= 0.201 Angle : 0.636 7.619 7105 Z= 0.328 Chirality : 0.042 0.186 805 Planarity : 0.005 0.076 848 Dihedral : 16.666 147.420 890 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.12 % Allowed : 11.75 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: 0.32 (0.34), residues: 623 helix: 1.35 (0.28), residues: 315 sheet: -0.88 (0.49), residues: 105 loop : -0.90 (0.47), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 47 HIS 0.005 0.001 HIS C 35 PHE 0.016 0.002 PHE B 70 TYR 0.012 0.001 TYR B 37 ARG 0.002 0.000 ARG A 140 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.563 Fit side-chains REVERT: A 112 GLU cc_start: 0.7428 (tt0) cc_final: 0.7210 (tt0) REVERT: A 137 GLU cc_start: 0.7871 (tp30) cc_final: 0.7351 (mm-30) REVERT: B 27 LYS cc_start: 0.8269 (mmmt) cc_final: 0.7825 (mtmt) REVERT: B 184 ILE cc_start: 0.8269 (mm) cc_final: 0.7944 (mt) REVERT: B 198 ARG cc_start: 0.8693 (ttm170) cc_final: 0.8454 (mtp85) REVERT: D 30 TYR cc_start: 0.8912 (m-80) cc_final: 0.8567 (m-80) outliers start: 6 outliers final: 3 residues processed: 89 average time/residue: 0.2157 time to fit residues: 23.8452 Evaluate side-chains 78 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 75 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain C residue 88 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 50 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.168975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.136613 restraints weight = 5911.759| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 2.20 r_work: 0.3573 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5237 Z= 0.269 Angle : 0.628 6.832 7105 Z= 0.320 Chirality : 0.043 0.191 805 Planarity : 0.005 0.081 848 Dihedral : 15.250 151.683 881 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.87 % Allowed : 13.25 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: 0.78 (0.35), residues: 623 helix: 1.88 (0.29), residues: 306 sheet: -0.76 (0.49), residues: 110 loop : -0.77 (0.49), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 47 HIS 0.006 0.001 HIS C 35 PHE 0.020 0.002 PHE D 91 TYR 0.015 0.001 TYR D 49 ARG 0.002 0.000 ARG A 140 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.571 Fit side-chains revert: symmetry clash REVERT: A 27 LYS cc_start: 0.8614 (tmmt) cc_final: 0.8128 (tptt) REVERT: A 88 ARG cc_start: 0.8042 (mtp-110) cc_final: 0.7775 (mmm-85) REVERT: A 137 GLU cc_start: 0.7886 (tp30) cc_final: 0.7133 (mm-30) REVERT: B 27 LYS cc_start: 0.8355 (mmmt) cc_final: 0.7987 (ttpt) REVERT: C 5 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7973 (tt0) REVERT: C 90 ASP cc_start: 0.8797 (m-30) cc_final: 0.8513 (m-30) REVERT: D 30 TYR cc_start: 0.8925 (m-80) cc_final: 0.8519 (m-80) outliers start: 10 outliers final: 5 residues processed: 82 average time/residue: 0.2259 time to fit residues: 22.8540 Evaluate side-chains 82 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain C residue 5 GLN Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain D residue 106 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 18 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 45 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.173409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.141149 restraints weight = 6041.075| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 2.20 r_work: 0.3622 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5237 Z= 0.222 Angle : 0.580 6.572 7105 Z= 0.293 Chirality : 0.041 0.194 805 Planarity : 0.005 0.079 848 Dihedral : 13.567 150.516 881 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.24 % Allowed : 13.81 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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 (0.36), residues: 623 helix: 2.17 (0.29), residues: 306 sheet: -0.82 (0.47), residues: 122 loop : -0.63 (0.51), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 47 HIS 0.004 0.001 HIS C 35 PHE 0.015 0.001 PHE B 70 TYR 0.014 0.001 TYR D 49 ARG 0.002 0.000 ARG B 198 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.587 Fit side-chains revert: symmetry clash REVERT: A 27 LYS cc_start: 0.8700 (tmmt) cc_final: 0.8166 (tptt) REVERT: A 88 ARG cc_start: 0.8057 (mtp-110) cc_final: 0.7807 (mmm-85) REVERT: A 137 GLU cc_start: 0.7891 (tp30) cc_final: 0.7231 (mm-30) REVERT: B 27 LYS cc_start: 0.8356 (mmmt) cc_final: 0.8018 (ttpt) REVERT: B 138 MET cc_start: 0.7835 (mtp) cc_final: 0.7600 (mtp) REVERT: C 5 GLN cc_start: 0.8209 (tt0) cc_final: 0.7971 (tt0) REVERT: C 90 ASP cc_start: 0.8799 (m-30) cc_final: 0.8530 (m-30) REVERT: D 71 TYR cc_start: 0.8598 (m-80) cc_final: 0.8160 (m-80) outliers start: 12 outliers final: 8 residues processed: 78 average time/residue: 0.1975 time to fit residues: 19.5906 Evaluate side-chains 80 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 106 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 0 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.173839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.142643 restraints weight = 5977.157| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 2.11 r_work: 0.3628 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5237 Z= 0.222 Angle : 0.567 6.617 7105 Z= 0.288 Chirality : 0.040 0.197 805 Planarity : 0.005 0.081 848 Dihedral : 12.393 149.578 881 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.43 % Allowed : 14.18 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.36), residues: 623 helix: 2.26 (0.29), residues: 306 sheet: -0.86 (0.47), residues: 122 loop : -0.61 (0.52), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 47 HIS 0.004 0.001 HIS C 35 PHE 0.016 0.001 PHE D 91 TYR 0.015 0.001 TYR D 49 ARG 0.004 0.000 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.554 Fit side-chains revert: symmetry clash REVERT: A 27 LYS cc_start: 0.8690 (tmmt) cc_final: 0.8123 (tptt) REVERT: A 88 ARG cc_start: 0.8088 (mtp-110) cc_final: 0.7884 (mmm-85) REVERT: A 137 GLU cc_start: 0.7874 (tp30) cc_final: 0.7223 (mm-30) REVERT: B 27 LYS cc_start: 0.8360 (mmmt) cc_final: 0.8003 (ttpt) REVERT: B 62 MET cc_start: 0.7241 (OUTLIER) cc_final: 0.7011 (ttm) REVERT: B 138 MET cc_start: 0.7839 (mtp) cc_final: 0.7609 (mtp) REVERT: C 5 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7913 (tt0) REVERT: C 90 ASP cc_start: 0.8847 (m-30) cc_final: 0.8539 (m-30) outliers start: 13 outliers final: 8 residues processed: 75 average time/residue: 0.1940 time to fit residues: 18.3853 Evaluate side-chains 78 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain C residue 5 GLN Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 97 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 9 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 182 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.172712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.140733 restraints weight = 6074.450| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 2.21 r_work: 0.3615 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5237 Z= 0.225 Angle : 0.559 6.236 7105 Z= 0.283 Chirality : 0.040 0.197 805 Planarity : 0.005 0.082 848 Dihedral : 11.845 152.918 881 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.43 % Allowed : 15.11 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.36), residues: 623 helix: 2.26 (0.29), residues: 306 sheet: -0.86 (0.47), residues: 122 loop : -0.65 (0.51), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 47 HIS 0.004 0.001 HIS C 35 PHE 0.015 0.001 PHE D 91 TYR 0.016 0.001 TYR D 49 ARG 0.003 0.000 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.541 Fit side-chains revert: symmetry clash REVERT: A 27 LYS cc_start: 0.8680 (tmmt) cc_final: 0.8120 (tptt) REVERT: A 137 GLU cc_start: 0.7880 (tp30) cc_final: 0.7193 (mm-30) REVERT: B 27 LYS cc_start: 0.8356 (mmmt) cc_final: 0.7992 (ttpt) REVERT: B 138 MET cc_start: 0.7906 (mtp) cc_final: 0.7690 (mtp) REVERT: C 5 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7935 (tt0) outliers start: 13 outliers final: 10 residues processed: 75 average time/residue: 0.2090 time to fit residues: 19.5780 Evaluate side-chains 79 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain C residue 5 GLN Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 97 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 182 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.170497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.138363 restraints weight = 5972.112| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.24 r_work: 0.3587 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5237 Z= 0.314 Angle : 0.618 6.970 7105 Z= 0.313 Chirality : 0.042 0.200 805 Planarity : 0.005 0.086 848 Dihedral : 11.759 166.282 881 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.80 % Allowed : 14.37 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: 0.86 (0.36), residues: 623 helix: 1.97 (0.29), residues: 306 sheet: -0.84 (0.47), residues: 125 loop : -0.65 (0.53), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 47 HIS 0.004 0.001 HIS B 186 PHE 0.020 0.002 PHE D 91 TYR 0.018 0.001 TYR D 49 ARG 0.003 0.001 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.527 Fit side-chains revert: symmetry clash REVERT: A 137 GLU cc_start: 0.7813 (tp30) cc_final: 0.7194 (mm-30) REVERT: A 172 PHE cc_start: 0.8026 (m-10) cc_final: 0.7777 (m-10) REVERT: B 27 LYS cc_start: 0.8384 (mmmt) cc_final: 0.8018 (ttpt) REVERT: B 138 MET cc_start: 0.7922 (mtp) cc_final: 0.7683 (mtt) REVERT: C 5 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7943 (tt0) REVERT: C 90 ASP cc_start: 0.8824 (m-30) cc_final: 0.8582 (m-30) REVERT: D 71 TYR cc_start: 0.8649 (m-80) cc_final: 0.8185 (m-80) outliers start: 15 outliers final: 12 residues processed: 80 average time/residue: 0.1923 time to fit residues: 19.3986 Evaluate side-chains 84 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 5 GLN Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 97 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 28 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 61 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 22 optimal weight: 0.1980 chunk 53 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 31 optimal weight: 0.0030 chunk 7 optimal weight: 0.6980 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.174949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.143346 restraints weight = 5999.022| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 2.20 r_work: 0.3653 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5237 Z= 0.157 Angle : 0.522 5.915 7105 Z= 0.264 Chirality : 0.039 0.193 805 Planarity : 0.005 0.080 848 Dihedral : 10.757 162.511 881 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.05 % Allowed : 15.11 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: 1.17 (0.36), residues: 623 helix: 2.37 (0.29), residues: 308 sheet: -0.42 (0.51), residues: 108 loop : -1.02 (0.48), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 47 HIS 0.004 0.001 HIS B 186 PHE 0.014 0.001 PHE A 39 TYR 0.012 0.001 TYR D 49 ARG 0.006 0.001 ARG A 88 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 LYS cc_start: 0.8672 (tmmt) cc_final: 0.8117 (tptt) REVERT: A 172 PHE cc_start: 0.7896 (m-10) cc_final: 0.7652 (m-10) REVERT: B 27 LYS cc_start: 0.8325 (mmmt) cc_final: 0.7995 (ttpt) REVERT: B 138 MET cc_start: 0.7925 (mtp) cc_final: 0.7672 (mtt) REVERT: C 32 TYR cc_start: 0.8271 (m-80) cc_final: 0.7969 (m-80) REVERT: D 100 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7973 (mm-30) outliers start: 11 outliers final: 10 residues processed: 76 average time/residue: 0.2093 time to fit residues: 20.1747 Evaluate side-chains 79 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 97 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 49 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.173229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.142136 restraints weight = 6008.788| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.16 r_work: 0.3626 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5237 Z= 0.222 Angle : 0.555 6.769 7105 Z= 0.281 Chirality : 0.040 0.195 805 Planarity : 0.005 0.083 848 Dihedral : 10.766 168.868 881 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.05 % Allowed : 15.49 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.36), residues: 623 helix: 2.33 (0.29), residues: 306 sheet: -0.70 (0.48), residues: 122 loop : -0.74 (0.51), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 47 HIS 0.003 0.001 HIS C 35 PHE 0.015 0.001 PHE D 91 TYR 0.015 0.001 TYR D 49 ARG 0.005 0.001 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.522 Fit side-chains revert: symmetry clash REVERT: A 27 LYS cc_start: 0.8682 (tmmt) cc_final: 0.8111 (tptt) REVERT: A 88 ARG cc_start: 0.8051 (mtp-110) cc_final: 0.7593 (mtp-110) REVERT: A 137 GLU cc_start: 0.7910 (tp30) cc_final: 0.7042 (mm-30) REVERT: A 172 PHE cc_start: 0.7930 (m-10) cc_final: 0.7681 (m-10) REVERT: B 27 LYS cc_start: 0.8313 (mmmt) cc_final: 0.7972 (ttpt) REVERT: B 138 MET cc_start: 0.7841 (mtp) cc_final: 0.7600 (mtt) REVERT: D 81 GLU cc_start: 0.7930 (pm20) cc_final: 0.7664 (pm20) outliers start: 11 outliers final: 11 residues processed: 76 average time/residue: 0.2088 time to fit residues: 19.9314 Evaluate side-chains 79 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 182 HIS ** D 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.171265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.140101 restraints weight = 6013.618| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 2.15 r_work: 0.3601 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5237 Z= 0.282 Angle : 0.598 6.644 7105 Z= 0.303 Chirality : 0.042 0.197 805 Planarity : 0.005 0.084 848 Dihedral : 11.090 178.685 881 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.05 % Allowed : 15.86 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: 1.01 (0.36), residues: 623 helix: 2.15 (0.29), residues: 306 sheet: -0.70 (0.48), residues: 122 loop : -0.74 (0.51), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 47 HIS 0.004 0.001 HIS B 48 PHE 0.017 0.002 PHE D 91 TYR 0.017 0.001 TYR D 49 ARG 0.004 0.001 ARG C 13 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: A 27 LYS cc_start: 0.8715 (tmmt) cc_final: 0.8146 (tptt) REVERT: A 88 ARG cc_start: 0.8068 (mtp-110) cc_final: 0.7786 (mtp-110) REVERT: A 137 GLU cc_start: 0.7976 (tp30) cc_final: 0.7292 (mm-30) REVERT: A 172 PHE cc_start: 0.8014 (m-10) cc_final: 0.7767 (m-10) REVERT: B 27 LYS cc_start: 0.8361 (mmmt) cc_final: 0.8003 (ttpt) REVERT: D 81 GLU cc_start: 0.7958 (pm20) cc_final: 0.7680 (pm20) outliers start: 11 outliers final: 11 residues processed: 76 average time/residue: 0.2005 time to fit residues: 19.1496 Evaluate side-chains 78 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 2 optimal weight: 0.4980 chunk 48 optimal weight: 3.9990 chunk 12 optimal weight: 0.4980 chunk 49 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 182 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.174401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.143272 restraints weight = 5994.160| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.23 r_work: 0.3511 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5237 Z= 0.206 Angle : 0.553 6.492 7105 Z= 0.281 Chirality : 0.040 0.192 805 Planarity : 0.005 0.082 848 Dihedral : 10.787 175.890 881 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.05 % Allowed : 16.60 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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 (0.36), residues: 623 helix: 2.30 (0.29), residues: 308 sheet: -0.39 (0.52), residues: 108 loop : -1.03 (0.47), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 47 HIS 0.003 0.001 HIS B 186 PHE 0.014 0.001 PHE A 39 TYR 0.014 0.001 TYR D 49 ARG 0.004 0.000 ARG C 13 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2691.05 seconds wall clock time: 47 minutes 0.21 seconds (2820.21 seconds total)