Starting phenix.real_space_refine on Fri Aug 22 14:39:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uc3_42114/08_2025/8uc3_42114.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uc3_42114/08_2025/8uc3_42114.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uc3_42114/08_2025/8uc3_42114.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uc3_42114/08_2025/8uc3_42114.map" model { file = "/net/cci-nas-00/data/ceres_data/8uc3_42114/08_2025/8uc3_42114.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uc3_42114/08_2025/8uc3_42114.cif" } resolution = 2.78 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.039 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 2 5.49 5 S 28 5.16 5 C 2700 2.51 5 N 766 2.21 5 O 808 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4304 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1365 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 13, 'TRANS': 166} Chain: "D" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 756 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 6, 'TRANS': 91} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C Time building chain proxies: 1.33, per 1000 atoms: 0.31 Number of scatterers: 4304 At special positions: 0 Unit cell: (84.87, 75.5343, 78.9291, 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 28 16.00 P 2 15.00 O 808 8.00 N 766 7.00 C 2700 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.37 Conformation dependent library (CDL) restraints added in 230.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1044 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 2 sheets defined 58.3% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 16 through 24 Processing helix chain 'A' and resid 36 through 48 Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 66 through 76 removed outlier: 3.801A pdb=" N ARG A 71 " --> pdb=" O PRO A 67 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE A 76 " --> pdb=" O ARG A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 97 No H-bonds generated for 'chain 'A' and resid 95 through 97' Processing helix chain 'A' and resid 101 through 130 removed outlier: 3.733A pdb=" N THR A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER A 112 " --> pdb=" O ILE A 108 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS A 113 " --> pdb=" O TYR A 109 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N MET A 118 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA A 119 " --> pdb=" O CYS A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 150 removed outlier: 3.503A pdb=" N VAL A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 181 removed outlier: 3.855A pdb=" N VAL A 181 " --> pdb=" O ALA A 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 177 through 181' Processing helix chain 'D' and resid 9 through 29 Processing helix chain 'D' and resid 37 through 55 removed outlier: 3.505A pdb=" N GLU D 55 " --> pdb=" O GLN D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 76 removed outlier: 3.732A pdb=" N ARG D 67 " --> pdb=" O LEU D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 99 Processing helix chain 'D' and resid 100 through 103 Processing helix chain 'C' and resid 9 through 29 Processing helix chain 'C' and resid 37 through 55 removed outlier: 3.505A pdb=" N GLU C 55 " --> pdb=" O GLN C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 76 removed outlier: 3.733A pdb=" N ARG C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 99 Processing helix chain 'C' and resid 100 through 103 Processing helix chain 'B' and resid 16 through 24 Processing helix chain 'B' and resid 36 through 48 Processing helix chain 'B' and resid 52 through 56 Processing helix chain 'B' and resid 66 through 76 removed outlier: 3.801A pdb=" N ARG B 71 " --> pdb=" O PRO B 67 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE B 76 " --> pdb=" O ARG B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 97 No H-bonds generated for 'chain 'B' and resid 95 through 97' Processing helix chain 'B' and resid 101 through 130 removed outlier: 3.733A pdb=" N THR B 111 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER B 112 " --> pdb=" O ILE B 108 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS B 113 " --> pdb=" O TYR B 109 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N MET B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA B 119 " --> pdb=" O CYS B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 150 removed outlier: 3.504A pdb=" N VAL B 145 " --> pdb=" O ARG B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 181 removed outlier: 3.855A pdb=" N VAL B 181 " --> pdb=" O ALA B 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 177 through 181' Processing sheet with id=AA1, first strand: chain 'A' and resid 133 through 134 removed outlier: 6.078A pdb=" N VAL A 92 " --> pdb=" O PRO A 157 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 182 through 184 removed outlier: 6.903A pdb=" N ASN A 183 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL B 92 " --> pdb=" O PRO B 157 " (cutoff:3.500A) 234 hydrogen bonds defined for protein. 672 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: 0.67 Time building geometry restraints manager: 0.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1176 1.33 - 1.45: 646 1.45 - 1.57: 2514 1.57 - 1.69: 2 1.69 - 1.81: 46 Bond restraints: 4384 Sorted by residual: bond pdb=" C4 FMN B 301 " pdb=" C4A FMN B 301 " ideal model delta sigma weight residual 1.485 1.387 0.098 2.00e-02 2.50e+03 2.38e+01 bond pdb=" C4 FMN A 301 " pdb=" C4A FMN A 301 " ideal model delta sigma weight residual 1.485 1.388 0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" C4A FMN A 301 " pdb=" N5 FMN A 301 " ideal model delta sigma weight residual 1.300 1.377 -0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" C4A FMN B 301 " pdb=" N5 FMN B 301 " ideal model delta sigma weight residual 1.300 1.377 -0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" N VAL B 182 " pdb=" CA VAL B 182 " ideal model delta sigma weight residual 1.458 1.500 -0.041 1.19e-02 7.06e+03 1.21e+01 ... (remaining 4379 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 5515 1.59 - 3.18: 372 3.18 - 4.77: 57 4.77 - 6.36: 16 6.36 - 7.95: 10 Bond angle restraints: 5970 Sorted by residual: angle pdb=" N THR B 23 " pdb=" CA THR B 23 " pdb=" C THR B 23 " ideal model delta sigma weight residual 112.54 118.53 -5.99 1.22e+00 6.72e-01 2.41e+01 angle pdb=" N THR A 23 " pdb=" CA THR A 23 " pdb=" C THR A 23 " ideal model delta sigma weight residual 112.54 118.49 -5.95 1.22e+00 6.72e-01 2.38e+01 angle pdb=" N ARG B 66 " pdb=" CA ARG B 66 " pdb=" C ARG B 66 " ideal model delta sigma weight residual 109.64 103.67 5.97 1.27e+00 6.20e-01 2.21e+01 angle pdb=" N ARG A 66 " pdb=" CA ARG A 66 " pdb=" C ARG A 66 " ideal model delta sigma weight residual 109.64 103.68 5.96 1.27e+00 6.20e-01 2.20e+01 angle pdb=" CA GLU A 180 " pdb=" C GLU A 180 " pdb=" O GLU A 180 " ideal model delta sigma weight residual 120.55 116.93 3.62 1.06e+00 8.90e-01 1.17e+01 ... (remaining 5965 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.90: 2347 16.90 - 33.79: 227 33.79 - 50.69: 94 50.69 - 67.58: 12 67.58 - 84.48: 8 Dihedral angle restraints: 2688 sinusoidal: 1080 harmonic: 1608 Sorted by residual: dihedral pdb=" CG ARG A 74 " pdb=" CD ARG A 74 " pdb=" NE ARG A 74 " pdb=" CZ ARG A 74 " ideal model delta sinusoidal sigma weight residual -180.00 -135.17 -44.83 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CG ARG B 74 " pdb=" CD ARG B 74 " pdb=" NE ARG B 74 " pdb=" CZ ARG B 74 " ideal model delta sinusoidal sigma weight residual 180.00 -135.19 -44.81 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CA ARG A 56 " pdb=" CB ARG A 56 " pdb=" CG ARG A 56 " pdb=" CD ARG A 56 " ideal model delta sinusoidal sigma weight residual -180.00 -125.98 -54.02 3 1.50e+01 4.44e-03 9.25e+00 ... (remaining 2685 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 536 0.050 - 0.100: 105 0.100 - 0.149: 45 0.149 - 0.199: 0 0.199 - 0.249: 2 Chirality restraints: 688 Sorted by residual: chirality pdb=" CA VAL A 64 " pdb=" N VAL A 64 " pdb=" C VAL A 64 " pdb=" CB VAL A 64 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA VAL B 64 " pdb=" N VAL B 64 " pdb=" C VAL B 64 " pdb=" CB VAL B 64 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CG LEU A 100 " pdb=" CB LEU A 100 " pdb=" CD1 LEU A 100 " pdb=" CD2 LEU A 100 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.50e-01 ... (remaining 685 not shown) Planarity restraints: 774 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 179 " -0.019 2.00e-02 2.50e+03 3.73e-02 1.39e+01 pdb=" C ASN A 179 " 0.064 2.00e-02 2.50e+03 pdb=" O ASN A 179 " -0.024 2.00e-02 2.50e+03 pdb=" N GLU A 180 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 179 " 0.018 2.00e-02 2.50e+03 3.71e-02 1.37e+01 pdb=" C ASN B 179 " -0.064 2.00e-02 2.50e+03 pdb=" O ASN B 179 " 0.024 2.00e-02 2.50e+03 pdb=" N GLU B 180 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 161 " 0.036 5.00e-02 4.00e+02 5.44e-02 4.74e+00 pdb=" N PRO B 162 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 162 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 162 " 0.030 5.00e-02 4.00e+02 ... (remaining 771 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 74 2.67 - 3.23: 4019 3.23 - 3.79: 6215 3.79 - 4.34: 8917 4.34 - 4.90: 14548 Nonbonded interactions: 33773 Sorted by model distance: nonbonded pdb=" OE2 GLU D 32 " pdb=" NH2 ARG B 141 " model vdw 2.115 3.120 nonbonded pdb=" OD1 ASP C 44 " pdb=" NH1 ARG C 47 " model vdw 2.321 3.120 nonbonded pdb=" OD1 ASP D 44 " pdb=" NH1 ARG D 47 " model vdw 2.321 3.120 nonbonded pdb=" NH2 ARG C 62 " pdb=" OE2 GLU C 101 " model vdw 2.343 3.120 nonbonded pdb=" NH2 ARG D 62 " pdb=" OE2 GLU D 101 " model vdw 2.343 3.120 ... (remaining 33768 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'D' selection = chain 'C' } 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: 3.200 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: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.330 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:6.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 4386 Z= 0.374 Angle : 0.919 7.947 5970 Z= 0.560 Chirality : 0.049 0.249 688 Planarity : 0.006 0.054 774 Dihedral : 16.352 84.478 1644 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.78 % Allowed : 22.67 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.36), residues: 548 helix: 0.58 (0.32), residues: 272 sheet: 2.34 (0.74), residues: 44 loop : -0.48 (0.42), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 69 TYR 0.009 0.001 TYR B 109 PHE 0.005 0.001 PHE B 86 TRP 0.009 0.002 TRP A 187 HIS 0.002 0.001 HIS B 154 Details of bonding type rmsd covalent geometry : bond 0.00614 ( 4384) covalent geometry : angle 0.91874 ( 5970) hydrogen bonds : bond 0.27114 ( 234) hydrogen bonds : angle 6.93495 ( 672) Misc. bond : bond 0.00104 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.156 Fit side-chains REVERT: C 62 ARG cc_start: 0.6692 (ttm170) cc_final: 0.6217 (mtp180) REVERT: C 94 GLN cc_start: 0.7342 (mt0) cc_final: 0.7056 (mt0) REVERT: B 118 MET cc_start: 0.7280 (mtt) cc_final: 0.6907 (mtt) outliers start: 8 outliers final: 2 residues processed: 89 average time/residue: 0.6188 time to fit residues: 56.8056 Evaluate side-chains 70 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 68 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 183 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.0000 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.183701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.142939 restraints weight = 4846.543| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 2.14 r_work: 0.3671 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3553 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4386 Z= 0.167 Angle : 0.646 6.735 5970 Z= 0.336 Chirality : 0.043 0.144 688 Planarity : 0.006 0.055 774 Dihedral : 6.321 55.530 633 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 6.22 % Allowed : 20.22 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.37), residues: 548 helix: 1.02 (0.30), residues: 292 sheet: 2.13 (0.76), residues: 54 loop : -0.53 (0.45), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 24 TYR 0.014 0.002 TYR D 22 PHE 0.006 0.001 PHE A 86 TRP 0.021 0.003 TRP B 18 HIS 0.002 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 4384) covalent geometry : angle 0.64593 ( 5970) hydrogen bonds : bond 0.06171 ( 234) hydrogen bonds : angle 4.31132 ( 672) Misc. bond : bond 0.00167 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 68 time to evaluate : 0.168 Fit side-chains REVERT: A 22 LYS cc_start: 0.6345 (mtmt) cc_final: 0.6092 (mptt) REVERT: A 56 ARG cc_start: 0.6606 (mtt180) cc_final: 0.6329 (mtm-85) REVERT: C 40 TYR cc_start: 0.7043 (m-80) cc_final: 0.6786 (m-80) REVERT: C 97 ASP cc_start: 0.7241 (m-30) cc_final: 0.6782 (m-30) REVERT: B 108 ILE cc_start: 0.7872 (pt) cc_final: 0.7665 (pp) REVERT: B 156 GLU cc_start: 0.7803 (tt0) cc_final: 0.7601 (tt0) REVERT: B 174 GLN cc_start: 0.7259 (tp40) cc_final: 0.7007 (tp40) outliers start: 28 outliers final: 10 residues processed: 83 average time/residue: 0.4831 time to fit residues: 41.6062 Evaluate side-chains 74 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 173 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 49 optimal weight: 1.9990 chunk 6 optimal weight: 0.0470 chunk 17 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 2 optimal weight: 0.3980 chunk 40 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 25 optimal weight: 5.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.185372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.144416 restraints weight = 4700.147| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 2.12 r_work: 0.3689 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3570 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4386 Z= 0.128 Angle : 0.570 10.472 5970 Z= 0.287 Chirality : 0.040 0.132 688 Planarity : 0.005 0.054 774 Dihedral : 5.941 58.831 633 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.67 % Allowed : 21.11 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.37), residues: 548 helix: 1.50 (0.30), residues: 292 sheet: 1.94 (0.78), residues: 54 loop : -0.30 (0.47), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 165 TYR 0.011 0.001 TYR D 22 PHE 0.009 0.001 PHE A 86 TRP 0.011 0.002 TRP B 18 HIS 0.003 0.001 HIS A 154 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 4384) covalent geometry : angle 0.56997 ( 5970) hydrogen bonds : bond 0.04885 ( 234) hydrogen bonds : angle 3.96358 ( 672) Misc. bond : bond 0.00121 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 68 time to evaluate : 0.106 Fit side-chains REVERT: A 22 LYS cc_start: 0.6296 (mtmt) cc_final: 0.6073 (mptt) REVERT: A 56 ARG cc_start: 0.6594 (mtt180) cc_final: 0.6324 (mtm-85) REVERT: D 33 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7770 (mt-10) REVERT: C 40 TYR cc_start: 0.6881 (m-80) cc_final: 0.6546 (m-80) REVERT: B 174 GLN cc_start: 0.7288 (tp40) cc_final: 0.6625 (mp10) outliers start: 21 outliers final: 10 residues processed: 78 average time/residue: 0.5467 time to fit residues: 44.1372 Evaluate side-chains 74 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 186 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 31 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 8 optimal weight: 0.0980 chunk 7 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.183088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.142960 restraints weight = 4647.859| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 2.04 r_work: 0.3671 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3554 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4386 Z= 0.138 Angle : 0.577 6.193 5970 Z= 0.294 Chirality : 0.041 0.137 688 Planarity : 0.006 0.057 774 Dihedral : 5.883 56.680 632 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 5.11 % Allowed : 19.78 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.37), residues: 548 helix: 1.57 (0.30), residues: 292 sheet: 1.94 (0.78), residues: 54 loop : -0.26 (0.47), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 165 TYR 0.011 0.001 TYR D 22 PHE 0.010 0.001 PHE A 86 TRP 0.013 0.002 TRP B 18 HIS 0.003 0.001 HIS A 154 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 4384) covalent geometry : angle 0.57706 ( 5970) hydrogen bonds : bond 0.05031 ( 234) hydrogen bonds : angle 4.00080 ( 672) Misc. bond : bond 0.00131 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 64 time to evaluate : 0.170 Fit side-chains REVERT: A 56 ARG cc_start: 0.6635 (mtt180) cc_final: 0.6370 (mtm-85) REVERT: D 33 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7716 (mt-10) REVERT: C 40 TYR cc_start: 0.6985 (m-80) cc_final: 0.6638 (m-80) REVERT: B 174 GLN cc_start: 0.7349 (tp40) cc_final: 0.6626 (mp10) outliers start: 23 outliers final: 13 residues processed: 75 average time/residue: 0.5242 time to fit residues: 40.7167 Evaluate side-chains 75 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 186 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 51 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 8 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- 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 = 0.3998 r_free = 0.3998 target = 0.172351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.131285 restraints weight = 4778.396| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.21 r_work: 0.3502 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 4386 Z= 0.242 Angle : 0.752 8.987 5970 Z= 0.382 Chirality : 0.047 0.180 688 Planarity : 0.007 0.069 774 Dihedral : 6.238 46.015 632 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 5.78 % Allowed : 18.67 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.36), residues: 548 helix: 1.01 (0.29), residues: 284 sheet: 1.54 (0.75), residues: 52 loop : -0.81 (0.44), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 165 TYR 0.012 0.002 TYR D 22 PHE 0.011 0.002 PHE A 86 TRP 0.024 0.004 TRP A 18 HIS 0.004 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00602 ( 4384) covalent geometry : angle 0.75219 ( 5970) hydrogen bonds : bond 0.07060 ( 234) hydrogen bonds : angle 4.52269 ( 672) Misc. bond : bond 0.00164 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 65 time to evaluate : 0.214 Fit side-chains REVERT: A 56 ARG cc_start: 0.6660 (mmt180) cc_final: 0.6344 (mtm-85) REVERT: A 62 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7696 (ttp) REVERT: A 147 SER cc_start: 0.7152 (t) cc_final: 0.6778 (p) REVERT: D 33 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7869 (mt-10) REVERT: C 36 ASP cc_start: 0.8173 (t0) cc_final: 0.6860 (t0) REVERT: C 40 TYR cc_start: 0.6846 (m-80) cc_final: 0.5933 (m-80) REVERT: B 161 VAL cc_start: 0.7346 (OUTLIER) cc_final: 0.7135 (t) REVERT: B 174 GLN cc_start: 0.7443 (tp40) cc_final: 0.5806 (pm20) outliers start: 26 outliers final: 14 residues processed: 79 average time/residue: 0.5306 time to fit residues: 43.4571 Evaluate side-chains 82 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 173 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 51 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 49 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4038 r_free = 0.4038 target = 0.176164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.135019 restraints weight = 4879.672| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.24 r_work: 0.3547 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4386 Z= 0.142 Angle : 0.595 6.113 5970 Z= 0.305 Chirality : 0.041 0.141 688 Planarity : 0.006 0.067 774 Dihedral : 5.690 47.943 632 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.00 % Allowed : 20.89 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.37), residues: 548 helix: 1.45 (0.30), residues: 290 sheet: 1.54 (0.76), residues: 52 loop : -0.49 (0.46), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 165 TYR 0.010 0.001 TYR C 22 PHE 0.011 0.001 PHE A 86 TRP 0.010 0.002 TRP B 18 HIS 0.002 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 4384) covalent geometry : angle 0.59474 ( 5970) hydrogen bonds : bond 0.05032 ( 234) hydrogen bonds : angle 4.02772 ( 672) Misc. bond : bond 0.00114 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.197 Fit side-chains REVERT: A 56 ARG cc_start: 0.6724 (mmt180) cc_final: 0.6387 (mtm-85) REVERT: A 62 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.7599 (ttp) REVERT: A 147 SER cc_start: 0.7131 (t) cc_final: 0.6787 (p) REVERT: D 33 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7722 (mt-10) REVERT: D 97 ASP cc_start: 0.7352 (m-30) cc_final: 0.6561 (m-30) REVERT: C 36 ASP cc_start: 0.8143 (t0) cc_final: 0.6874 (t0) REVERT: C 40 TYR cc_start: 0.6800 (m-80) cc_final: 0.5956 (m-80) REVERT: B 174 GLN cc_start: 0.7437 (tp40) cc_final: 0.5832 (pm20) outliers start: 18 outliers final: 10 residues processed: 74 average time/residue: 0.5862 time to fit residues: 44.8623 Evaluate side-chains 75 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 173 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 26 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 13 optimal weight: 0.0070 chunk 10 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 52 optimal weight: 0.0470 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.178743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.137674 restraints weight = 4841.930| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.21 r_work: 0.3576 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3457 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4386 Z= 0.117 Angle : 0.551 6.458 5970 Z= 0.282 Chirality : 0.039 0.134 688 Planarity : 0.006 0.068 774 Dihedral : 5.324 49.101 630 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.56 % Allowed : 20.89 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.37), residues: 548 helix: 1.76 (0.30), residues: 290 sheet: 1.57 (0.76), residues: 52 loop : -0.27 (0.48), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A 165 TYR 0.009 0.001 TYR D 22 PHE 0.009 0.001 PHE A 86 TRP 0.007 0.001 TRP B 18 HIS 0.003 0.001 HIS A 154 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 4384) covalent geometry : angle 0.55082 ( 5970) hydrogen bonds : bond 0.04280 ( 234) hydrogen bonds : angle 3.76385 ( 672) Misc. bond : bond 0.00093 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.179 Fit side-chains REVERT: A 18 TRP cc_start: 0.6119 (OUTLIER) cc_final: 0.5584 (m-90) REVERT: A 56 ARG cc_start: 0.6725 (mmt180) cc_final: 0.6400 (mtm-85) REVERT: A 62 MET cc_start: 0.7929 (OUTLIER) cc_final: 0.7611 (ttp) REVERT: A 147 SER cc_start: 0.7166 (t) cc_final: 0.6821 (p) REVERT: D 33 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7650 (mt-10) REVERT: C 36 ASP cc_start: 0.8154 (t0) cc_final: 0.6940 (t0) REVERT: C 40 TYR cc_start: 0.6764 (m-80) cc_final: 0.5929 (m-80) REVERT: B 45 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6752 (tt0) REVERT: B 174 GLN cc_start: 0.7453 (tp40) cc_final: 0.5859 (pm20) outliers start: 16 outliers final: 8 residues processed: 75 average time/residue: 0.6049 time to fit residues: 46.7921 Evaluate side-chains 75 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 TRP Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 173 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 46 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 53 optimal weight: 0.0570 chunk 13 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.178851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.137658 restraints weight = 4759.361| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.21 r_work: 0.3569 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3451 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4386 Z= 0.125 Angle : 0.568 6.578 5970 Z= 0.291 Chirality : 0.040 0.136 688 Planarity : 0.006 0.079 774 Dihedral : 5.317 48.709 630 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.89 % Allowed : 22.22 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.37), residues: 548 helix: 1.80 (0.30), residues: 290 sheet: 1.15 (0.74), residues: 54 loop : -0.17 (0.49), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 165 TYR 0.009 0.001 TYR D 22 PHE 0.010 0.001 PHE A 86 TRP 0.008 0.001 TRP B 18 HIS 0.003 0.001 HIS A 154 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 4384) covalent geometry : angle 0.56835 ( 5970) hydrogen bonds : bond 0.04464 ( 234) hydrogen bonds : angle 3.81192 ( 672) Misc. bond : bond 0.00100 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.208 Fit side-chains REVERT: A 56 ARG cc_start: 0.6772 (mmt180) cc_final: 0.6471 (mtm-85) REVERT: A 62 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.7622 (ttp) REVERT: A 147 SER cc_start: 0.7141 (t) cc_final: 0.6792 (p) REVERT: D 33 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7627 (mt-10) REVERT: D 72 GLU cc_start: 0.7197 (tm-30) cc_final: 0.6075 (mt-10) REVERT: C 36 ASP cc_start: 0.8147 (t0) cc_final: 0.6844 (t0) REVERT: C 40 TYR cc_start: 0.6729 (m-80) cc_final: 0.5901 (m-80) REVERT: B 174 GLN cc_start: 0.7506 (tp40) cc_final: 0.5793 (pm20) outliers start: 13 outliers final: 10 residues processed: 74 average time/residue: 0.5570 time to fit residues: 42.6445 Evaluate side-chains 73 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 186 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 3 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 0.0170 chunk 19 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 overall best weight: 0.8820 ------------------------------------------------------------------------------- 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 = 0.4048 r_free = 0.4048 target = 0.176968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.135544 restraints weight = 4852.518| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.23 r_work: 0.3557 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4386 Z= 0.146 Angle : 0.616 6.873 5970 Z= 0.313 Chirality : 0.041 0.142 688 Planarity : 0.006 0.086 774 Dihedral : 5.402 47.855 630 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.78 % Allowed : 20.44 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.37), residues: 548 helix: 1.67 (0.30), residues: 290 sheet: 1.12 (0.75), residues: 54 loop : -0.20 (0.49), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 165 TYR 0.009 0.002 TYR D 22 PHE 0.010 0.001 PHE A 86 TRP 0.012 0.002 TRP A 18 HIS 0.002 0.001 HIS B 128 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 4384) covalent geometry : angle 0.61586 ( 5970) hydrogen bonds : bond 0.04993 ( 234) hydrogen bonds : angle 3.97187 ( 672) Misc. bond : bond 0.00117 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.193 Fit side-chains REVERT: A 56 ARG cc_start: 0.6620 (mmt180) cc_final: 0.6306 (mtm-85) REVERT: A 62 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7634 (ttp) REVERT: A 147 SER cc_start: 0.7117 (t) cc_final: 0.6766 (p) REVERT: A 158 MET cc_start: 0.7613 (OUTLIER) cc_final: 0.7293 (ttt) REVERT: D 33 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7571 (mt-10) REVERT: C 36 ASP cc_start: 0.8171 (t0) cc_final: 0.6880 (t0) REVERT: C 40 TYR cc_start: 0.6740 (m-80) cc_final: 0.5899 (m-80) REVERT: B 62 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.8135 (ttm) REVERT: B 174 GLN cc_start: 0.7506 (tp40) cc_final: 0.5771 (pm20) outliers start: 17 outliers final: 13 residues processed: 70 average time/residue: 0.5578 time to fit residues: 40.3856 Evaluate side-chains 77 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 186 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 7 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 37 optimal weight: 0.5980 chunk 21 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4060 r_free = 0.4060 target = 0.178126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.136593 restraints weight = 4783.332| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 2.24 r_work: 0.3562 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4386 Z= 0.132 Angle : 0.594 7.100 5970 Z= 0.305 Chirality : 0.040 0.137 688 Planarity : 0.006 0.089 774 Dihedral : 5.351 48.262 630 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.78 % Allowed : 20.22 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.38), residues: 548 helix: 1.75 (0.30), residues: 290 sheet: 1.13 (0.75), residues: 54 loop : -0.15 (0.49), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 165 TYR 0.009 0.001 TYR C 22 PHE 0.010 0.001 PHE A 86 TRP 0.010 0.001 TRP B 18 HIS 0.002 0.001 HIS A 154 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 4384) covalent geometry : angle 0.59426 ( 5970) hydrogen bonds : bond 0.04636 ( 234) hydrogen bonds : angle 3.87852 ( 672) Misc. bond : bond 0.00105 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.113 Fit side-chains REVERT: A 56 ARG cc_start: 0.6706 (mmt180) cc_final: 0.6385 (mtm-85) REVERT: A 62 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.7626 (ttp) REVERT: A 147 SER cc_start: 0.7217 (t) cc_final: 0.6874 (p) REVERT: D 33 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7576 (mt-10) REVERT: C 36 ASP cc_start: 0.8155 (t0) cc_final: 0.6863 (t0) REVERT: C 40 TYR cc_start: 0.6757 (m-80) cc_final: 0.5943 (m-80) REVERT: C 95 MET cc_start: 0.5374 (mmm) cc_final: 0.4356 (tpt) REVERT: B 174 GLN cc_start: 0.7509 (tp40) cc_final: 0.5802 (pm20) outliers start: 17 outliers final: 12 residues processed: 71 average time/residue: 0.4776 time to fit residues: 35.2362 Evaluate side-chains 75 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 186 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 17 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 6 optimal weight: 0.0470 chunk 9 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.7478 ------------------------------------------------------------------------------- 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 = 0.4061 r_free = 0.4061 target = 0.177977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.136494 restraints weight = 4806.761| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.24 r_work: 0.3564 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3445 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4386 Z= 0.136 Angle : 0.601 7.070 5970 Z= 0.307 Chirality : 0.040 0.139 688 Planarity : 0.006 0.089 774 Dihedral : 5.371 48.093 630 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.56 % Allowed : 20.67 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.38), residues: 548 helix: 1.74 (0.30), residues: 290 sheet: 1.22 (0.75), residues: 54 loop : -0.15 (0.49), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 165 TYR 0.009 0.001 TYR C 22 PHE 0.010 0.001 PHE A 86 TRP 0.010 0.001 TRP B 18 HIS 0.002 0.001 HIS B 154 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 4384) covalent geometry : angle 0.60054 ( 5970) hydrogen bonds : bond 0.04760 ( 234) hydrogen bonds : angle 3.88182 ( 672) Misc. bond : bond 0.00109 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1726.09 seconds wall clock time: 30 minutes 6.10 seconds (1806.10 seconds total)