Starting phenix.real_space_refine on Sat May 10 00:02:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uc3_42114/05_2025/8uc3_42114.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uc3_42114/05_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_42114/05_2025/8uc3_42114.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uc3_42114/05_2025/8uc3_42114.map" model { file = "/net/cci-nas-00/data/ceres_data/8uc3_42114/05_2025/8uc3_42114.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uc3_42114/05_2025/8uc3_42114.cif" } resolution = 2.78 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.039 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: "C" 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: D, B Time building chain proxies: 3.65, per 1000 atoms: 0.85 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: 1.19 Conformation dependent library (CDL) restraints added in 556.8 milliseconds 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: 0.46 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: 1.09 Time building geometry restraints manager: 1.33 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: 0.02 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } 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: 2.840 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 15.470 Find NCS groups from input model: 0.090 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:11.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.630 ------------------------------------------------------------------------------- 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 (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: 0.37 (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 TRP 0.009 0.002 TRP A 187 HIS 0.002 0.001 HIS B 154 PHE 0.005 0.001 PHE B 86 TYR 0.009 0.001 TYR B 109 ARG 0.004 0.001 ARG C 69 Details of bonding type rmsd hydrogen bonds : bond 0.27114 ( 234) hydrogen bonds : angle 6.93495 ( 672) covalent geometry : bond 0.00614 ( 4384) covalent geometry : angle 0.91874 ( 5970) 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 : 0.479 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: 1.2989 time to fit residues: 119.6512 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 : 0.495 ------------------------------------------------------------------------------- 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 45 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 25 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4248 r_free = 0.4248 target = 0.189846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.151160 restraints weight = 4783.696| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 2.01 r_work: 0.3785 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3672 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4386 Z= 0.155 Angle : 0.633 6.697 5970 Z= 0.329 Chirality : 0.043 0.142 688 Planarity : 0.006 0.054 774 Dihedral : 6.314 56.174 633 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 6.67 % Allowed : 19.56 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.88 (0.37), residues: 548 helix: 1.03 (0.30), residues: 294 sheet: 2.11 (0.76), residues: 54 loop : -0.44 (0.45), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 18 HIS 0.002 0.001 HIS A 154 PHE 0.006 0.001 PHE A 86 TYR 0.014 0.002 TYR D 22 ARG 0.003 0.001 ARG C 62 Details of bonding type rmsd hydrogen bonds : bond 0.05612 ( 234) hydrogen bonds : angle 4.21824 ( 672) covalent geometry : bond 0.00344 ( 4384) covalent geometry : angle 0.63254 ( 5970) Misc. bond : bond 0.00161 ( 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 97 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 67 time to evaluate : 0.439 Fit side-chains REVERT: D 33 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7946 (mt-10) REVERT: C 40 TYR cc_start: 0.7202 (m-80) cc_final: 0.6979 (m-80) REVERT: C 97 ASP cc_start: 0.7330 (m-30) cc_final: 0.6896 (m-30) REVERT: B 174 GLN cc_start: 0.7309 (tp40) cc_final: 0.7075 (tp40) outliers start: 30 outliers final: 10 residues processed: 83 average time/residue: 1.0227 time to fit residues: 88.4789 Evaluate side-chains 75 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 17 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 8 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4152 r_free = 0.4152 target = 0.183392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.142339 restraints weight = 4655.045| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.10 r_work: 0.3656 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3538 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.2816 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= 0.146 Angle : 0.612 11.140 5970 Z= 0.308 Chirality : 0.041 0.135 688 Planarity : 0.006 0.057 774 Dihedral : 6.024 56.912 633 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 5.11 % Allowed : 20.22 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.37), residues: 548 helix: 1.51 (0.31), residues: 288 sheet: 1.97 (0.77), residues: 54 loop : -0.48 (0.45), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 18 HIS 0.003 0.001 HIS A 154 PHE 0.010 0.001 PHE A 86 TYR 0.012 0.002 TYR D 22 ARG 0.014 0.001 ARG A 165 Details of bonding type rmsd hydrogen bonds : bond 0.05470 ( 234) hydrogen bonds : angle 4.12023 ( 672) covalent geometry : bond 0.00334 ( 4384) covalent geometry : angle 0.61237 ( 5970) Misc. bond : bond 0.00146 ( 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 91 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 0.441 Fit side-chains REVERT: A 22 LYS cc_start: 0.6204 (mptt) cc_final: 0.5921 (mmtm) REVERT: A 56 ARG cc_start: 0.6596 (mtt180) cc_final: 0.6353 (mtm-85) REVERT: D 33 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7812 (mt-10) REVERT: C 40 TYR cc_start: 0.6997 (m-80) cc_final: 0.6629 (m-80) REVERT: B 174 GLN cc_start: 0.7358 (tp40) cc_final: 0.6678 (mp10) outliers start: 23 outliers final: 12 residues processed: 79 average time/residue: 1.1796 time to fit residues: 96.6002 Evaluate side-chains 74 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU 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 D residue 39 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 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 2 optimal weight: 0.1980 chunk 51 optimal weight: 3.9990 chunk 52 optimal weight: 0.1980 chunk 39 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.4180 r_free = 0.4180 target = 0.185782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.144529 restraints weight = 4708.297| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 2.12 r_work: 0.3686 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3568 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4386 Z= 0.117 Angle : 0.542 5.736 5970 Z= 0.277 Chirality : 0.039 0.133 688 Planarity : 0.005 0.056 774 Dihedral : 5.809 56.208 632 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.00 % Allowed : 20.67 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.38), residues: 548 helix: 1.72 (0.30), residues: 292 sheet: 1.88 (0.77), residues: 54 loop : -0.14 (0.48), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 18 HIS 0.003 0.001 HIS A 154 PHE 0.009 0.001 PHE A 86 TYR 0.010 0.001 TYR D 22 ARG 0.014 0.001 ARG A 165 Details of bonding type rmsd hydrogen bonds : bond 0.04385 ( 234) hydrogen bonds : angle 3.79725 ( 672) covalent geometry : bond 0.00260 ( 4384) covalent geometry : angle 0.54241 ( 5970) Misc. bond : bond 0.00109 ( 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 82 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.432 Fit side-chains REVERT: A 22 LYS cc_start: 0.6153 (mttt) cc_final: 0.5857 (mmtm) REVERT: A 56 ARG cc_start: 0.6610 (mtt180) cc_final: 0.6353 (mtm-85) REVERT: A 62 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.7744 (ttp) REVERT: D 33 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7766 (mt-10) REVERT: C 40 TYR cc_start: 0.6938 (m-80) cc_final: 0.6584 (m-80) REVERT: B 174 GLN cc_start: 0.7352 (tp40) cc_final: 0.6635 (mp10) outliers start: 18 outliers final: 8 residues processed: 72 average time/residue: 1.3034 time to fit residues: 97.0369 Evaluate side-chains 71 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain D residue 33 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 148 MET 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 25 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 16 optimal weight: 0.0070 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 15 optimal weight: 0.0670 overall best weight: 0.4936 ------------------------------------------------------------------------------- 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 = 0.4084 r_free = 0.4084 target = 0.180734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.138606 restraints weight = 4812.041| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.26 r_work: 0.3587 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4386 Z= 0.114 Angle : 0.534 5.491 5970 Z= 0.274 Chirality : 0.039 0.134 688 Planarity : 0.005 0.060 774 Dihedral : 5.704 53.448 632 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.67 % Allowed : 19.56 % 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 (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: 1.69 (0.38), residues: 548 helix: 1.87 (0.30), residues: 292 sheet: 1.60 (0.78), residues: 54 loop : -0.07 (0.49), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 18 HIS 0.003 0.001 HIS A 154 PHE 0.009 0.001 PHE A 86 TYR 0.009 0.001 TYR D 22 ARG 0.015 0.000 ARG A 165 Details of bonding type rmsd hydrogen bonds : bond 0.04276 ( 234) hydrogen bonds : angle 3.74175 ( 672) covalent geometry : bond 0.00255 ( 4384) covalent geometry : angle 0.53391 ( 5970) Misc. bond : bond 0.00099 ( 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 83 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 62 time to evaluate : 0.494 Fit side-chains REVERT: A 22 LYS cc_start: 0.5847 (mttt) cc_final: 0.5598 (mmtm) REVERT: A 56 ARG cc_start: 0.6613 (mtt180) cc_final: 0.6331 (mtm-85) REVERT: A 62 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7636 (ttp) REVERT: A 109 TYR cc_start: 0.7501 (t80) cc_final: 0.7260 (t80) REVERT: D 33 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7662 (mt-10) REVERT: C 40 TYR cc_start: 0.6804 (m-80) cc_final: 0.6455 (m-80) REVERT: B 174 GLN cc_start: 0.7291 (tp40) cc_final: 0.5839 (pm20) outliers start: 21 outliers final: 13 residues processed: 73 average time/residue: 1.2617 time to fit residues: 95.4690 Evaluate side-chains 75 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 92 VAL 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 91 CYS Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 186 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 47 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.1980 chunk 35 optimal weight: 2.9990 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 = 0.4065 r_free = 0.4065 target = 0.179158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.136291 restraints weight = 4795.091| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.30 r_work: 0.3567 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4386 Z= 0.130 Angle : 0.570 6.007 5970 Z= 0.290 Chirality : 0.040 0.139 688 Planarity : 0.006 0.067 774 Dihedral : 5.639 48.230 632 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 5.11 % Allowed : 19.33 % 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 (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: 1.60 (0.38), residues: 548 helix: 1.84 (0.30), residues: 290 sheet: 1.48 (0.78), residues: 54 loop : -0.14 (0.48), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 18 HIS 0.002 0.001 HIS A 154 PHE 0.010 0.001 PHE A 86 TYR 0.010 0.001 TYR D 22 ARG 0.015 0.001 ARG A 165 Details of bonding type rmsd hydrogen bonds : bond 0.04680 ( 234) hydrogen bonds : angle 3.85101 ( 672) covalent geometry : bond 0.00302 ( 4384) covalent geometry : angle 0.56972 ( 5970) Misc. bond : bond 0.00112 ( 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 85 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 62 time to evaluate : 0.436 Fit side-chains REVERT: A 22 LYS cc_start: 0.5876 (mttt) cc_final: 0.5584 (mmtm) REVERT: A 56 ARG cc_start: 0.6528 (mtt180) cc_final: 0.6223 (mtm-85) REVERT: D 33 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7600 (mt-10) REVERT: D 72 GLU cc_start: 0.7087 (tm-30) cc_final: 0.5914 (mt-10) REVERT: C 40 TYR cc_start: 0.6716 (m-80) cc_final: 0.5951 (m-80) REVERT: B 174 GLN cc_start: 0.7375 (tp40) cc_final: 0.5869 (pm20) outliers start: 23 outliers final: 14 residues processed: 75 average time/residue: 1.3133 time to fit residues: 101.8487 Evaluate side-chains 74 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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 47 MET Chi-restraints excluded: chain A residue 91 CYS 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 12 optimal weight: 0.5980 chunk 32 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4057 r_free = 0.4057 target = 0.178117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.136461 restraints weight = 4808.290| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.23 r_work: 0.3565 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3448 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.3521 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= 0.134 Angle : 0.575 6.223 5970 Z= 0.294 Chirality : 0.040 0.138 688 Planarity : 0.006 0.075 774 Dihedral : 5.522 48.224 632 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.78 % Allowed : 20.67 % 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 (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: 1.59 (0.37), residues: 548 helix: 1.84 (0.30), residues: 290 sheet: 1.38 (0.76), residues: 54 loop : -0.13 (0.48), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 18 HIS 0.002 0.001 HIS A 154 PHE 0.010 0.001 PHE A 86 TYR 0.009 0.001 TYR D 22 ARG 0.017 0.001 ARG A 165 Details of bonding type rmsd hydrogen bonds : bond 0.04726 ( 234) hydrogen bonds : angle 3.87109 ( 672) covalent geometry : bond 0.00314 ( 4384) covalent geometry : angle 0.57483 ( 5970) Misc. bond : bond 0.00109 ( 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 77 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.478 Fit side-chains REVERT: A 22 LYS cc_start: 0.5981 (mttt) cc_final: 0.5668 (mmtm) REVERT: A 56 ARG cc_start: 0.6640 (mmt180) cc_final: 0.6340 (mtm-85) REVERT: A 147 SER cc_start: 0.7115 (t) cc_final: 0.6761 (p) REVERT: D 33 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7655 (mt-10) REVERT: C 36 ASP cc_start: 0.8142 (t0) cc_final: 0.6689 (t0) REVERT: C 40 TYR cc_start: 0.6854 (m-80) cc_final: 0.5952 (m-80) REVERT: B 174 GLN cc_start: 0.7461 (tp40) cc_final: 0.5871 (pm20) outliers start: 17 outliers final: 13 residues processed: 69 average time/residue: 1.2996 time to fit residues: 92.7605 Evaluate side-chains 74 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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 47 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 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 Chi-restraints excluded: chain B residue 186 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 50 optimal weight: 0.4980 chunk 19 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 29 optimal weight: 0.1980 chunk 26 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.4085 r_free = 0.4085 target = 0.180708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.138099 restraints weight = 4733.869| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.30 r_work: 0.3591 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.3611 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= 0.117 Angle : 0.550 6.570 5970 Z= 0.282 Chirality : 0.039 0.135 688 Planarity : 0.006 0.076 774 Dihedral : 5.240 48.969 630 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.00 % Allowed : 20.44 % 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 (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: 1.76 (0.38), residues: 548 helix: 1.99 (0.30), residues: 290 sheet: 1.34 (0.76), residues: 54 loop : -0.02 (0.49), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 18 HIS 0.003 0.001 HIS A 154 PHE 0.009 0.001 PHE A 86 TYR 0.009 0.001 TYR D 22 ARG 0.019 0.000 ARG A 165 Details of bonding type rmsd hydrogen bonds : bond 0.04208 ( 234) hydrogen bonds : angle 3.71774 ( 672) covalent geometry : bond 0.00267 ( 4384) covalent geometry : angle 0.55017 ( 5970) Misc. bond : bond 0.00097 ( 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 78 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.501 Fit side-chains REVERT: A 22 LYS cc_start: 0.5785 (mttt) cc_final: 0.5503 (mmtm) REVERT: A 56 ARG cc_start: 0.6665 (mmt180) cc_final: 0.6340 (mtm-85) REVERT: A 147 SER cc_start: 0.7049 (t) cc_final: 0.6694 (p) REVERT: A 158 MET cc_start: 0.7490 (OUTLIER) cc_final: 0.7122 (ttt) REVERT: D 33 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7579 (mt-10) REVERT: C 40 TYR cc_start: 0.6784 (m-80) cc_final: 0.6096 (m-80) REVERT: B 174 GLN cc_start: 0.7486 (tp40) cc_final: 0.5891 (pm20) outliers start: 18 outliers final: 11 residues processed: 69 average time/residue: 1.2632 time to fit residues: 90.2686 Evaluate side-chains 70 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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 47 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 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 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 29 optimal weight: 0.3980 chunk 39 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.4050 r_free = 0.4050 target = 0.177609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.134762 restraints weight = 4843.180| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.31 r_work: 0.3545 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4386 Z= 0.154 Angle : 0.614 7.263 5970 Z= 0.314 Chirality : 0.041 0.145 688 Planarity : 0.006 0.087 774 Dihedral : 5.407 48.007 630 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.78 % Allowed : 20.89 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.37), residues: 548 helix: 1.76 (0.30), residues: 290 sheet: 1.18 (0.75), residues: 54 loop : -0.17 (0.49), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 18 HIS 0.003 0.001 HIS B 128 PHE 0.010 0.001 PHE A 86 TYR 0.011 0.002 TYR D 22 ARG 0.020 0.001 ARG A 165 Details of bonding type rmsd hydrogen bonds : bond 0.05245 ( 234) hydrogen bonds : angle 4.00706 ( 672) covalent geometry : bond 0.00370 ( 4384) covalent geometry : angle 0.61448 ( 5970) Misc. bond : bond 0.00125 ( 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 77 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.521 Fit side-chains REVERT: A 56 ARG cc_start: 0.6696 (mmt180) cc_final: 0.6408 (mtm-85) REVERT: A 62 MET cc_start: 0.7911 (OUTLIER) cc_final: 0.7585 (ttp) REVERT: A 147 SER cc_start: 0.7063 (t) cc_final: 0.6702 (p) REVERT: D 33 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7605 (mt-10) REVERT: D 72 GLU cc_start: 0.7232 (tm-30) cc_final: 0.5995 (mt-10) REVERT: D 90 ASP cc_start: 0.6316 (t70) cc_final: 0.5849 (t0) REVERT: C 36 ASP cc_start: 0.8162 (t0) cc_final: 0.6769 (t0) REVERT: C 40 TYR cc_start: 0.6791 (m-80) cc_final: 0.5925 (m-80) REVERT: B 174 GLN cc_start: 0.7478 (tp40) cc_final: 0.5756 (pm20) outliers start: 17 outliers final: 11 residues processed: 70 average time/residue: 1.2360 time to fit residues: 89.8229 Evaluate side-chains 73 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.435 ------------------------------------------------------------------------------- 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 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 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 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 4 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 3 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 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 = 0.4067 r_free = 0.4067 target = 0.179161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.136146 restraints weight = 4725.120| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.30 r_work: 0.3567 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3448 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.3798 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= 0.131 Angle : 0.583 7.058 5970 Z= 0.297 Chirality : 0.040 0.132 688 Planarity : 0.006 0.089 774 Dihedral : 5.340 48.172 630 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.33 % Allowed : 20.67 % 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 (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: 1.56 (0.38), residues: 548 helix: 1.87 (0.30), residues: 290 sheet: 1.07 (0.76), residues: 54 loop : -0.14 (0.49), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 18 HIS 0.002 0.001 HIS B 128 PHE 0.010 0.001 PHE A 86 TYR 0.008 0.001 TYR C 22 ARG 0.020 0.001 ARG A 165 Details of bonding type rmsd hydrogen bonds : bond 0.04661 ( 234) hydrogen bonds : angle 3.90395 ( 672) covalent geometry : bond 0.00303 ( 4384) covalent geometry : angle 0.58252 ( 5970) 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 75 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.463 Fit side-chains REVERT: A 56 ARG cc_start: 0.6705 (mmt180) cc_final: 0.6389 (mtm-85) REVERT: A 62 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7570 (ttp) REVERT: A 147 SER cc_start: 0.7092 (t) cc_final: 0.6743 (p) REVERT: D 33 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7569 (mt-10) REVERT: D 72 GLU cc_start: 0.7229 (tm-30) cc_final: 0.5989 (mt-10) REVERT: C 36 ASP cc_start: 0.8143 (t0) cc_final: 0.6766 (t0) REVERT: C 40 TYR cc_start: 0.6787 (m-80) cc_final: 0.5962 (m-80) REVERT: C 95 MET cc_start: 0.5239 (mmm) cc_final: 0.4244 (tpt) REVERT: B 174 GLN cc_start: 0.7468 (tp40) cc_final: 0.5756 (pm20) outliers start: 15 outliers final: 11 residues processed: 68 average time/residue: 1.2329 time to fit residues: 86.9332 Evaluate side-chains 74 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.483 ------------------------------------------------------------------------------- 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 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 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 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 53 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 40 optimal weight: 0.0570 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 0.2980 chunk 4 optimal weight: 0.9980 chunk 18 optimal weight: 0.2980 chunk 2 optimal weight: 0.8980 overall best weight: 0.4698 ------------------------------------------------------------------------------- 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 = 0.4089 r_free = 0.4089 target = 0.181114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.138457 restraints weight = 4758.566| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 2.28 r_work: 0.3590 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.3883 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= 0.115 Angle : 0.555 7.197 5970 Z= 0.283 Chirality : 0.039 0.128 688 Planarity : 0.006 0.087 774 Dihedral : 5.253 49.051 630 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.44 % Allowed : 22.00 % 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 (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: 1.76 (0.38), residues: 548 helix: 2.04 (0.31), residues: 290 sheet: 1.18 (0.76), residues: 54 loop : -0.06 (0.49), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 18 HIS 0.002 0.001 HIS A 154 PHE 0.009 0.001 PHE A 86 TYR 0.007 0.001 TYR C 22 ARG 0.020 0.000 ARG A 165 Details of bonding type rmsd hydrogen bonds : bond 0.04120 ( 234) hydrogen bonds : angle 3.74403 ( 672) covalent geometry : bond 0.00260 ( 4384) covalent geometry : angle 0.55453 ( 5970) Misc. bond : bond 0.00092 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3763.28 seconds wall clock time: 65 minutes 52.13 seconds (3952.13 seconds total)