Starting phenix.real_space_refine on Wed Mar 12 01:25:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lq5_23481/03_2025/7lq5_23481.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lq5_23481/03_2025/7lq5_23481.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lq5_23481/03_2025/7lq5_23481.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lq5_23481/03_2025/7lq5_23481.map" model { file = "/net/cci-nas-00/data/ceres_data/7lq5_23481/03_2025/7lq5_23481.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lq5_23481/03_2025/7lq5_23481.cif" } resolution = 3.4 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= 0.001 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 Fe 24 7.16 5 S 54 5.16 5 C 4410 2.51 5 N 1140 2.21 5 O 1215 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6843 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1937 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 22, 'TRANS': 235} Chain: "A" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 344 Unusual residues: {'HEC': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Restraints were copied for chains: C, B Time building chain proxies: 4.90, per 1000 atoms: 0.72 Number of scatterers: 6843 At special positions: 0 Unit cell: (75.348, 61.272, 205.344, 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) Fe 24 26.01 S 54 16.00 O 1215 8.00 N 1140 7.00 C 4410 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=72, symmetry=0 Number of additional bonds: simple=72, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.07 Conformation dependent library (CDL) restraints added in 919.1 milliseconds 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1422 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 6 sheets defined 17.8% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 18 through 22 Processing helix chain 'A' and resid 32 through 42 removed outlier: 4.919A pdb=" N GLN A 38 " --> pdb=" O THR A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 46 Processing helix chain 'A' and resid 153 through 157 Processing helix chain 'A' and resid 189 through 194 removed outlier: 4.060A pdb=" N CYS A 193 " --> pdb=" O ASP A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 215 Processing helix chain 'A' and resid 244 through 252 removed outlier: 3.578A pdb=" N CYS A 248 " --> pdb=" O ASN A 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 22 Processing helix chain 'B' and resid 32 through 42 removed outlier: 4.919A pdb=" N GLN B 38 " --> pdb=" O THR B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 46 Processing helix chain 'B' and resid 153 through 157 Processing helix chain 'B' and resid 189 through 194 removed outlier: 4.060A pdb=" N CYS B 193 " --> pdb=" O ASP B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 215 Processing helix chain 'B' and resid 244 through 252 removed outlier: 3.579A pdb=" N CYS B 248 " --> pdb=" O ASN B 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 22 Processing helix chain 'C' and resid 32 through 42 removed outlier: 4.919A pdb=" N GLN C 38 " --> pdb=" O THR C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 46 Processing helix chain 'C' and resid 153 through 157 Processing helix chain 'C' and resid 189 through 194 removed outlier: 4.060A pdb=" N CYS C 193 " --> pdb=" O ASP C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 215 Processing helix chain 'C' and resid 244 through 252 removed outlier: 3.579A pdb=" N CYS C 248 " --> pdb=" O ASN C 244 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 71 through 74 removed outlier: 6.354A pdb=" N VAL A 72 " --> pdb=" O PHE A 79 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N PHE A 79 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY A 77 " --> pdb=" O ASP A 74 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 139 through 142 Processing sheet with id=AA3, first strand: chain 'B' and resid 71 through 74 removed outlier: 6.354A pdb=" N VAL B 72 " --> pdb=" O PHE B 79 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N PHE B 79 " --> pdb=" O VAL B 72 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY B 77 " --> pdb=" O ASP B 74 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 139 through 142 Processing sheet with id=AA5, first strand: chain 'C' and resid 71 through 74 removed outlier: 6.354A pdb=" N VAL C 72 " --> pdb=" O PHE C 79 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N PHE C 79 " --> pdb=" O VAL C 72 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY C 77 " --> pdb=" O ASP C 74 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 139 through 142 69 hydrogen bonds defined for protein. 153 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: 1.45 Time building geometry restraints manager: 2.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.38: 2867 1.38 - 1.56: 4150 1.56 - 1.73: 15 1.73 - 1.90: 60 1.90 - 2.08: 96 Bond restraints: 7188 Sorted by residual: bond pdb=" N VAL C 230 " pdb=" CA VAL C 230 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.30e+00 bond pdb=" N VAL A 230 " pdb=" CA VAL A 230 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.96e+00 bond pdb=" N VAL B 230 " pdb=" CA VAL B 230 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.73e+00 bond pdb=" N SER B 177 " pdb=" CA SER B 177 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.27e-02 6.20e+03 7.56e+00 bond pdb=" N SER A 177 " pdb=" CA SER A 177 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.27e-02 6.20e+03 7.50e+00 ... (remaining 7183 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 8027 1.41 - 2.82: 1705 2.82 - 4.23: 352 4.23 - 5.64: 71 5.64 - 7.05: 36 Bond angle restraints: 10191 Sorted by residual: angle pdb=" N ASP C 220 " pdb=" CA ASP C 220 " pdb=" C ASP C 220 " ideal model delta sigma weight residual 110.53 116.76 -6.23 1.32e+00 5.74e-01 2.23e+01 angle pdb=" N ASP A 220 " pdb=" CA ASP A 220 " pdb=" C ASP A 220 " ideal model delta sigma weight residual 110.53 116.74 -6.21 1.32e+00 5.74e-01 2.21e+01 angle pdb=" N ASP B 220 " pdb=" CA ASP B 220 " pdb=" C ASP B 220 " ideal model delta sigma weight residual 110.53 116.73 -6.20 1.32e+00 5.74e-01 2.21e+01 angle pdb=" N SER B 221 " pdb=" CA SER B 221 " pdb=" C SER B 221 " ideal model delta sigma weight residual 110.07 115.15 -5.08 1.26e+00 6.30e-01 1.63e+01 angle pdb=" N SER A 221 " pdb=" CA SER A 221 " pdb=" C SER A 221 " ideal model delta sigma weight residual 110.07 115.14 -5.07 1.26e+00 6.30e-01 1.62e+01 ... (remaining 10186 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.68: 3054 16.68 - 33.36: 435 33.36 - 50.04: 135 50.04 - 66.72: 30 66.72 - 83.40: 36 Dihedral angle restraints: 3690 sinusoidal: 1485 harmonic: 2205 Sorted by residual: dihedral pdb=" CA HIS C 30 " pdb=" C HIS C 30 " pdb=" N VAL C 31 " pdb=" CA VAL C 31 " ideal model delta harmonic sigma weight residual -180.00 -150.54 -29.46 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA HIS A 30 " pdb=" C HIS A 30 " pdb=" N VAL A 31 " pdb=" CA VAL A 31 " ideal model delta harmonic sigma weight residual -180.00 -150.55 -29.45 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA HIS B 30 " pdb=" C HIS B 30 " pdb=" N VAL B 31 " pdb=" CA VAL B 31 " ideal model delta harmonic sigma weight residual -180.00 -150.58 -29.42 0 5.00e+00 4.00e-02 3.46e+01 ... (remaining 3687 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 512 0.054 - 0.107: 288 0.107 - 0.161: 106 0.161 - 0.214: 6 0.214 - 0.267: 3 Chirality restraints: 915 Sorted by residual: chirality pdb=" CB THR B 94 " pdb=" CA THR B 94 " pdb=" OG1 THR B 94 " pdb=" CG2 THR B 94 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CB THR C 94 " pdb=" CA THR C 94 " pdb=" OG1 THR C 94 " pdb=" CG2 THR C 94 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CB THR A 94 " pdb=" CA THR A 94 " pdb=" OG1 THR A 94 " pdb=" CG2 THR A 94 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 912 not shown) Planarity restraints: 1251 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" ND HEC B 303 " 0.004 2.00e-02 2.50e+03 1.43e-02 4.58e+00 pdb=" C1D HEC B 303 " -0.001 2.00e-02 2.50e+03 pdb=" C2D HEC B 303 " 0.032 2.00e-02 2.50e+03 pdb=" C3D HEC B 303 " -0.016 2.00e-02 2.50e+03 pdb=" C4D HEC B 303 " -0.006 2.00e-02 2.50e+03 pdb=" CAD HEC B 303 " 0.012 2.00e-02 2.50e+03 pdb=" CHA HEC B 303 " -0.005 2.00e-02 2.50e+03 pdb=" CHD HEC B 303 " -0.000 2.00e-02 2.50e+03 pdb=" CMD HEC B 303 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND HEC C 303 " 0.004 2.00e-02 2.50e+03 1.42e-02 4.56e+00 pdb=" C1D HEC C 303 " -0.001 2.00e-02 2.50e+03 pdb=" C2D HEC C 303 " 0.031 2.00e-02 2.50e+03 pdb=" C3D HEC C 303 " -0.015 2.00e-02 2.50e+03 pdb=" C4D HEC C 303 " -0.007 2.00e-02 2.50e+03 pdb=" CAD HEC C 303 " 0.012 2.00e-02 2.50e+03 pdb=" CHA HEC C 303 " -0.005 2.00e-02 2.50e+03 pdb=" CHD HEC C 303 " 0.000 2.00e-02 2.50e+03 pdb=" CMD HEC C 303 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 166 " 0.011 2.00e-02 2.50e+03 2.13e-02 4.55e+00 pdb=" C ASP B 166 " -0.037 2.00e-02 2.50e+03 pdb=" O ASP B 166 " 0.014 2.00e-02 2.50e+03 pdb=" N PRO B 167 " 0.012 2.00e-02 2.50e+03 ... (remaining 1248 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 66 2.47 - 3.07: 4978 3.07 - 3.68: 10864 3.68 - 4.29: 15990 4.29 - 4.90: 25619 Nonbonded interactions: 57517 Sorted by model distance: nonbonded pdb=" NE2 HIS C 194 " pdb="FE HEC C 306 " model vdw 1.857 3.080 nonbonded pdb=" NE2 HIS B 194 " pdb="FE HEC B 306 " model vdw 1.858 3.080 nonbonded pdb=" NE2 HIS A 194 " pdb="FE HEC A 306 " model vdw 1.858 3.080 nonbonded pdb=" NE2 HIS A 158 " pdb="FE HEC A 305 " model vdw 2.009 3.080 nonbonded pdb=" NE2 HIS C 158 " pdb="FE HEC C 305 " model vdw 2.009 3.080 ... (remaining 57512 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' 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: 2.330 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 18.940 Find NCS groups from input model: 0.130 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: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 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 : 0.013 0.119 7188 Z= 0.826 Angle : 1.307 7.053 10191 Z= 0.644 Chirality : 0.068 0.267 915 Planarity : 0.009 0.044 1251 Dihedral : 19.666 83.396 2268 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 27.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.89 % Favored : 87.11 % Rotamer: Outliers : 0.45 % Allowed : 30.32 % Favored : 69.23 % 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: -4.95 (0.24), residues: 768 helix: -4.81 (0.13), residues: 126 sheet: None (None), residues: 0 loop : -3.31 (0.21), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.007 TRP A 239 HIS 0.022 0.005 HIS C 97 PHE 0.020 0.005 PHE B 176 TYR 0.015 0.006 TYR C 109 ARG 0.008 0.003 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 107 time to evaluate : 0.642 Fit side-chains REVERT: A 219 LYS cc_start: 0.7796 (tptt) cc_final: 0.6999 (mmtt) REVERT: A 245 ASN cc_start: 0.8347 (t0) cc_final: 0.8035 (t0) REVERT: B 128 SER cc_start: 0.8252 (m) cc_final: 0.7899 (p) outliers start: 3 outliers final: 3 residues processed: 109 average time/residue: 0.1932 time to fit residues: 28.2964 Evaluate side-chains 71 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 68 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 TRP Chi-restraints excluded: chain B residue 255 TRP Chi-restraints excluded: chain C residue 255 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 19 optimal weight: 10.0000 chunk 38 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 HIS B 199 ASN ** B 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 HIS C 199 ASN C 245 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.122806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.096342 restraints weight = 9984.477| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.71 r_work: 0.3246 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 7188 Z= 0.302 Angle : 0.929 12.159 10191 Z= 0.358 Chirality : 0.052 0.209 915 Planarity : 0.006 0.047 1251 Dihedral : 18.304 88.872 993 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.55 % Favored : 89.45 % Rotamer: Outliers : 5.88 % Allowed : 25.04 % Favored : 69.08 % 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: -3.62 (0.27), residues: 768 helix: -3.85 (0.28), residues: 108 sheet: None (None), residues: 0 loop : -2.39 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 255 HIS 0.007 0.001 HIS B 91 PHE 0.016 0.002 PHE B 10 TYR 0.009 0.001 TYR C 109 ARG 0.004 0.001 ARG B 173 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 80 time to evaluate : 0.522 Fit side-chains REVERT: A 15 ASP cc_start: 0.7563 (OUTLIER) cc_final: 0.6867 (t70) REVERT: A 239 TRP cc_start: 0.8452 (m100) cc_final: 0.8047 (m100) REVERT: B 15 ASP cc_start: 0.6948 (OUTLIER) cc_final: 0.6433 (t0) REVERT: B 128 SER cc_start: 0.8462 (m) cc_final: 0.8020 (p) REVERT: C 37 VAL cc_start: 0.8759 (m) cc_final: 0.8550 (t) REVERT: C 231 LYS cc_start: 0.7597 (mtmt) cc_final: 0.7341 (mmtm) REVERT: C 255 TRP cc_start: 0.7621 (OUTLIER) cc_final: 0.7310 (p90) outliers start: 39 outliers final: 24 residues processed: 111 average time/residue: 0.1632 time to fit residues: 25.1357 Evaluate side-chains 94 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 67 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 255 TRP Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 255 TRP Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 191 ASN Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 255 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 43 optimal weight: 0.4980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.2980 chunk 23 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 12 optimal weight: 0.0070 chunk 70 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 HIS B 245 ASN C 199 ASN ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.124611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.098678 restraints weight = 9890.688| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.67 r_work: 0.3283 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7188 Z= 0.244 Angle : 0.878 13.759 10191 Z= 0.327 Chirality : 0.050 0.159 915 Planarity : 0.005 0.045 1251 Dihedral : 18.086 87.693 993 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.46 % Favored : 88.54 % Rotamer: Outliers : 5.73 % Allowed : 29.41 % Favored : 64.86 % 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: -3.57 (0.28), residues: 768 helix: -3.56 (0.29), residues: 144 sheet: None (None), residues: 0 loop : -2.29 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 255 HIS 0.004 0.001 HIS B 91 PHE 0.010 0.001 PHE B 10 TYR 0.015 0.001 TYR C 109 ARG 0.003 0.001 ARG B 173 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 86 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.7306 (OUTLIER) cc_final: 0.6618 (t70) REVERT: A 231 LYS cc_start: 0.8656 (mppt) cc_final: 0.8426 (mttt) REVERT: A 239 TRP cc_start: 0.8325 (m100) cc_final: 0.7920 (m100) REVERT: A 255 TRP cc_start: 0.7453 (OUTLIER) cc_final: 0.6353 (p90) REVERT: B 15 ASP cc_start: 0.6785 (OUTLIER) cc_final: 0.6393 (m-30) REVERT: B 110 CYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7938 (p) REVERT: B 128 SER cc_start: 0.8389 (m) cc_final: 0.7928 (p) REVERT: C 64 LEU cc_start: 0.7793 (tp) cc_final: 0.7484 (tt) REVERT: C 231 LYS cc_start: 0.7669 (mtmt) cc_final: 0.7273 (mmtm) outliers start: 38 outliers final: 28 residues processed: 115 average time/residue: 0.1646 time to fit residues: 26.4294 Evaluate side-chains 104 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 72 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 96 HIS Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 208 CYS Chi-restraints excluded: chain A residue 255 TRP Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 208 CYS Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 245 ASN Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 255 TRP Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 191 ASN Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 208 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 0 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 51 optimal weight: 0.0060 chunk 24 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 overall best weight: 1.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 ASN ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.120493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.094069 restraints weight = 10142.148| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.73 r_work: 0.3212 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 7188 Z= 0.368 Angle : 1.027 17.112 10191 Z= 0.357 Chirality : 0.052 0.137 915 Planarity : 0.006 0.043 1251 Dihedral : 18.160 88.200 991 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.67 % Favored : 86.33 % Rotamer: Outliers : 7.24 % Allowed : 29.41 % Favored : 63.35 % 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: -3.59 (0.28), residues: 768 helix: -3.56 (0.29), residues: 144 sheet: None (None), residues: 0 loop : -2.30 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 255 HIS 0.007 0.001 HIS B 158 PHE 0.029 0.002 PHE C 10 TYR 0.013 0.002 TYR C 109 ARG 0.003 0.001 ARG B 173 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 87 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.7663 (OUTLIER) cc_final: 0.7016 (t70) REVERT: A 173 ARG cc_start: 0.7869 (mtp85) cc_final: 0.7183 (mtp180) REVERT: A 236 ASP cc_start: 0.6959 (t0) cc_final: 0.6570 (t0) REVERT: A 239 TRP cc_start: 0.8417 (m100) cc_final: 0.7871 (m100) REVERT: A 255 TRP cc_start: 0.7564 (OUTLIER) cc_final: 0.6999 (p90) REVERT: B 15 ASP cc_start: 0.7263 (OUTLIER) cc_final: 0.6211 (t70) REVERT: B 110 CYS cc_start: 0.8288 (OUTLIER) cc_final: 0.8056 (p) REVERT: B 128 SER cc_start: 0.8459 (m) cc_final: 0.8186 (t) REVERT: B 166 ASP cc_start: 0.8233 (m-30) cc_final: 0.7253 (t0) REVERT: B 214 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8425 (tt) REVERT: C 64 LEU cc_start: 0.7818 (tp) cc_final: 0.7511 (tt) outliers start: 48 outliers final: 37 residues processed: 125 average time/residue: 0.1539 time to fit residues: 27.0533 Evaluate side-chains 119 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 77 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 29 CYS Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 96 HIS Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 208 CYS Chi-restraints excluded: chain A residue 255 TRP Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 191 ASN Chi-restraints excluded: chain B residue 208 CYS Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 255 TRP Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 87 CYS Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 191 ASN Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 208 CYS Chi-restraints excluded: chain C residue 255 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 1 optimal weight: 0.6980 chunk 44 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 47 optimal weight: 0.0070 chunk 46 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 58 optimal weight: 0.4980 chunk 28 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 ASN ** C 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.123240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.096972 restraints weight = 9934.750| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.69 r_work: 0.3259 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 7188 Z= 0.262 Angle : 0.909 15.280 10191 Z= 0.330 Chirality : 0.049 0.139 915 Planarity : 0.005 0.044 1251 Dihedral : 17.840 89.332 991 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.98 % Favored : 88.02 % Rotamer: Outliers : 7.39 % Allowed : 29.56 % Favored : 63.05 % 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: -2.88 (0.29), residues: 768 helix: -3.09 (0.38), residues: 117 sheet: None (None), residues: 0 loop : -1.86 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 255 HIS 0.004 0.001 HIS B 158 PHE 0.018 0.001 PHE C 10 TYR 0.013 0.001 TYR C 109 ARG 0.002 0.000 ARG B 173 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 88 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.7417 (OUTLIER) cc_final: 0.6704 (t70) REVERT: A 231 LYS cc_start: 0.8709 (mppt) cc_final: 0.8486 (mttt) REVERT: A 249 GLN cc_start: 0.8545 (mt0) cc_final: 0.8329 (mt0) REVERT: A 255 TRP cc_start: 0.7430 (OUTLIER) cc_final: 0.7136 (p90) REVERT: B 15 ASP cc_start: 0.6942 (OUTLIER) cc_final: 0.6462 (t0) REVERT: B 110 CYS cc_start: 0.8295 (OUTLIER) cc_final: 0.8074 (p) REVERT: B 128 SER cc_start: 0.8339 (m) cc_final: 0.8033 (t) REVERT: B 139 ARG cc_start: 0.8005 (ptt90) cc_final: 0.7788 (ptt90) REVERT: B 166 ASP cc_start: 0.8083 (m-30) cc_final: 0.7180 (t0) REVERT: C 64 LEU cc_start: 0.7940 (tp) cc_final: 0.7622 (tt) outliers start: 49 outliers final: 37 residues processed: 128 average time/residue: 0.1470 time to fit residues: 26.5769 Evaluate side-chains 120 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 79 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 29 CYS Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 96 HIS Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 208 CYS Chi-restraints excluded: chain A residue 255 TRP Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 147 ASN Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 208 CYS Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 255 TRP Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 87 CYS Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 191 ASN Chi-restraints excluded: chain C residue 208 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 1.9990 chunk 12 optimal weight: 0.1980 chunk 55 optimal weight: 10.0000 chunk 44 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 43 optimal weight: 0.2980 chunk 61 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 ASN ** C 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.122860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.096239 restraints weight = 10059.473| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.73 r_work: 0.3249 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 7188 Z= 0.281 Angle : 0.946 16.102 10191 Z= 0.339 Chirality : 0.050 0.230 915 Planarity : 0.005 0.045 1251 Dihedral : 17.592 89.891 991 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.54 % Favored : 86.46 % Rotamer: Outliers : 8.45 % Allowed : 28.81 % Favored : 62.75 % 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: -2.81 (0.29), residues: 768 helix: -2.96 (0.39), residues: 117 sheet: None (None), residues: 0 loop : -1.83 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 255 HIS 0.004 0.001 HIS A 158 PHE 0.015 0.002 PHE C 10 TYR 0.012 0.001 TYR C 109 ARG 0.002 0.000 ARG B 173 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 86 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 GLN cc_start: 0.8532 (mt0) cc_final: 0.8306 (mt0) REVERT: A 255 TRP cc_start: 0.7311 (OUTLIER) cc_final: 0.7111 (p90) REVERT: B 15 ASP cc_start: 0.6935 (OUTLIER) cc_final: 0.5943 (t70) REVERT: B 110 CYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7977 (p) REVERT: B 128 SER cc_start: 0.8324 (m) cc_final: 0.8060 (t) REVERT: B 155 GLU cc_start: 0.8271 (tp30) cc_final: 0.8068 (tp30) REVERT: B 166 ASP cc_start: 0.8091 (m-30) cc_final: 0.7189 (t0) REVERT: B 255 TRP cc_start: 0.7709 (OUTLIER) cc_final: 0.7047 (p90) REVERT: C 64 LEU cc_start: 0.7941 (tp) cc_final: 0.7624 (tt) outliers start: 56 outliers final: 40 residues processed: 130 average time/residue: 0.1687 time to fit residues: 31.3715 Evaluate side-chains 122 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 78 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 29 CYS Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 96 HIS Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 208 CYS Chi-restraints excluded: chain A residue 255 TRP Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 147 ASN Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 191 ASN Chi-restraints excluded: chain B residue 208 CYS Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 255 TRP Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 87 CYS Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 191 ASN Chi-restraints excluded: chain C residue 208 CYS Chi-restraints excluded: chain C residue 255 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.122972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.096580 restraints weight = 9963.387| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.66 r_work: 0.3253 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 7188 Z= 0.296 Angle : 0.971 16.242 10191 Z= 0.350 Chirality : 0.051 0.178 915 Planarity : 0.005 0.047 1251 Dihedral : 17.398 89.458 991 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.80 % Favored : 86.20 % Rotamer: Outliers : 6.94 % Allowed : 28.81 % Favored : 64.25 % 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: -2.77 (0.29), residues: 768 helix: -2.96 (0.38), residues: 117 sheet: None (None), residues: 0 loop : -1.80 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 255 HIS 0.005 0.001 HIS B 252 PHE 0.012 0.002 PHE C 10 TYR 0.015 0.001 TYR C 109 ARG 0.003 0.001 ARG B 85 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 81 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 LYS cc_start: 0.7957 (tptt) cc_final: 0.6999 (mptt) REVERT: A 249 GLN cc_start: 0.8631 (mt0) cc_final: 0.8386 (mt0) REVERT: B 15 ASP cc_start: 0.7089 (OUTLIER) cc_final: 0.6026 (t70) REVERT: B 110 CYS cc_start: 0.8312 (OUTLIER) cc_final: 0.8064 (p) REVERT: B 128 SER cc_start: 0.8436 (m) cc_final: 0.8193 (t) REVERT: B 166 ASP cc_start: 0.8214 (m-30) cc_final: 0.7223 (t0) REVERT: B 255 TRP cc_start: 0.7777 (OUTLIER) cc_final: 0.7114 (p90) REVERT: C 64 LEU cc_start: 0.7874 (tp) cc_final: 0.7548 (tt) outliers start: 46 outliers final: 37 residues processed: 117 average time/residue: 0.1593 time to fit residues: 25.8437 Evaluate side-chains 116 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 76 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 96 HIS Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 208 CYS Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 147 ASN Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 191 ASN Chi-restraints excluded: chain B residue 208 CYS Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 248 CYS Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 255 TRP Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 87 CYS Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain C residue 191 ASN Chi-restraints excluded: chain C residue 208 CYS Chi-restraints excluded: chain C residue 234 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 31 optimal weight: 0.0980 chunk 33 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3717 r_free = 0.3717 target = 0.121493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.095174 restraints weight = 10120.159| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.68 r_work: 0.3229 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 7188 Z= 0.332 Angle : 1.016 16.706 10191 Z= 0.359 Chirality : 0.051 0.180 915 Planarity : 0.006 0.047 1251 Dihedral : 17.215 89.278 989 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.58 % Favored : 85.42 % Rotamer: Outliers : 6.79 % Allowed : 28.96 % Favored : 64.25 % 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: -2.86 (0.29), residues: 768 helix: -3.07 (0.36), residues: 117 sheet: None (None), residues: 0 loop : -1.85 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 255 HIS 0.005 0.001 HIS B 158 PHE 0.014 0.002 PHE C 10 TYR 0.015 0.002 TYR C 109 ARG 0.002 0.000 ARG B 173 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 79 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 LYS cc_start: 0.7985 (tptt) cc_final: 0.6960 (mptt) REVERT: B 15 ASP cc_start: 0.7257 (OUTLIER) cc_final: 0.6208 (t70) REVERT: B 110 CYS cc_start: 0.8272 (OUTLIER) cc_final: 0.8026 (p) REVERT: B 128 SER cc_start: 0.8492 (m) cc_final: 0.8230 (t) REVERT: B 166 ASP cc_start: 0.8247 (m-30) cc_final: 0.7228 (t0) REVERT: B 214 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8385 (tt) REVERT: B 255 TRP cc_start: 0.7758 (OUTLIER) cc_final: 0.7102 (p90) REVERT: C 64 LEU cc_start: 0.7855 (tp) cc_final: 0.7564 (tt) outliers start: 45 outliers final: 37 residues processed: 115 average time/residue: 0.1527 time to fit residues: 24.9792 Evaluate side-chains 113 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 72 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 96 HIS Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 208 CYS Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 147 ASN Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 191 ASN Chi-restraints excluded: chain B residue 208 CYS Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 248 CYS Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 255 TRP Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 87 CYS Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain C residue 191 ASN Chi-restraints excluded: chain C residue 208 CYS Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 248 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 23 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 117 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.121587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.095348 restraints weight = 10124.121| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.65 r_work: 0.3237 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 7188 Z= 0.322 Angle : 1.005 16.435 10191 Z= 0.359 Chirality : 0.051 0.174 915 Planarity : 0.006 0.061 1251 Dihedral : 17.272 89.551 989 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.06 % Favored : 85.94 % Rotamer: Outliers : 7.09 % Allowed : 28.51 % Favored : 64.40 % 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: -3.03 (0.28), residues: 768 helix: -3.06 (0.34), residues: 126 sheet: None (None), residues: 0 loop : -1.97 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 255 HIS 0.006 0.001 HIS B 158 PHE 0.018 0.002 PHE A 256 TYR 0.016 0.002 TYR C 109 ARG 0.002 0.000 ARG A 173 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 76 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.7466 (OUTLIER) cc_final: 0.6824 (t70) REVERT: A 173 ARG cc_start: 0.7495 (mtt180) cc_final: 0.6877 (mtp180) REVERT: A 219 LYS cc_start: 0.8076 (tptt) cc_final: 0.6959 (mptt) REVERT: B 15 ASP cc_start: 0.7276 (OUTLIER) cc_final: 0.6297 (t70) REVERT: B 110 CYS cc_start: 0.8268 (OUTLIER) cc_final: 0.8038 (p) REVERT: B 128 SER cc_start: 0.8467 (m) cc_final: 0.8239 (t) REVERT: B 214 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8405 (tt) REVERT: B 237 LEU cc_start: 0.7932 (tt) cc_final: 0.7532 (tp) REVERT: B 255 TRP cc_start: 0.7746 (OUTLIER) cc_final: 0.7088 (p90) REVERT: C 64 LEU cc_start: 0.7891 (tp) cc_final: 0.7675 (tt) REVERT: C 130 SER cc_start: 0.8466 (m) cc_final: 0.8072 (t) outliers start: 47 outliers final: 40 residues processed: 112 average time/residue: 0.1464 time to fit residues: 23.4287 Evaluate side-chains 112 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 67 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 96 HIS Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 208 CYS Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 147 ASN Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 191 ASN Chi-restraints excluded: chain B residue 208 CYS Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 248 CYS Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 255 TRP Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 87 CYS Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain C residue 191 ASN Chi-restraints excluded: chain C residue 208 CYS Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 248 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 30 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 12 optimal weight: 0.2980 chunk 61 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.123157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.097099 restraints weight = 10216.678| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.69 r_work: 0.3266 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 7188 Z= 0.274 Angle : 0.956 15.829 10191 Z= 0.349 Chirality : 0.050 0.174 915 Planarity : 0.006 0.058 1251 Dihedral : 17.061 89.023 989 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.54 % Favored : 86.46 % Rotamer: Outliers : 7.09 % Allowed : 28.81 % Favored : 64.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.29), residues: 768 helix: -2.81 (0.38), residues: 117 sheet: None (None), residues: 0 loop : -1.80 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 255 HIS 0.004 0.001 HIS B 158 PHE 0.018 0.002 PHE A 256 TYR 0.022 0.001 TYR C 109 ARG 0.003 0.000 ARG B 173 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 75 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.7324 (OUTLIER) cc_final: 0.6644 (t70) REVERT: A 173 ARG cc_start: 0.7472 (mtt180) cc_final: 0.6893 (mtp180) REVERT: A 219 LYS cc_start: 0.8011 (tptt) cc_final: 0.6932 (mptt) REVERT: B 15 ASP cc_start: 0.7191 (OUTLIER) cc_final: 0.6199 (t70) REVERT: B 110 CYS cc_start: 0.8264 (OUTLIER) cc_final: 0.8032 (p) REVERT: B 128 SER cc_start: 0.8505 (m) cc_final: 0.8268 (t) REVERT: B 237 LEU cc_start: 0.7833 (tt) cc_final: 0.7433 (tp) REVERT: B 255 TRP cc_start: 0.7711 (OUTLIER) cc_final: 0.7164 (p90) REVERT: C 130 SER cc_start: 0.8413 (m) cc_final: 0.8001 (t) outliers start: 47 outliers final: 39 residues processed: 111 average time/residue: 0.1546 time to fit residues: 24.9077 Evaluate side-chains 114 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 71 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 96 HIS Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 208 CYS Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 147 ASN Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 191 ASN Chi-restraints excluded: chain B residue 208 CYS Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 248 CYS Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 255 TRP Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 87 CYS Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain C residue 191 ASN Chi-restraints excluded: chain C residue 208 CYS Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 248 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 29 optimal weight: 0.3980 chunk 22 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 71 optimal weight: 0.7980 chunk 63 optimal weight: 0.0570 chunk 48 optimal weight: 0.8980 chunk 55 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 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 89 ASN ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.123233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.097429 restraints weight = 10069.030| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.64 r_work: 0.3275 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7188 Z= 0.270 Angle : 0.968 15.876 10191 Z= 0.350 Chirality : 0.050 0.166 915 Planarity : 0.006 0.058 1251 Dihedral : 17.019 89.426 989 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.28 % Favored : 86.72 % Rotamer: Outliers : 6.79 % Allowed : 29.26 % Favored : 63.95 % 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: -2.62 (0.29), residues: 768 helix: -2.35 (0.43), residues: 99 sheet: None (None), residues: 0 loop : -1.83 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 255 HIS 0.007 0.001 HIS B 252 PHE 0.012 0.002 PHE C 256 TYR 0.021 0.001 TYR C 109 ARG 0.002 0.000 ARG B 173 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3502.08 seconds wall clock time: 60 minutes 53.96 seconds (3653.96 seconds total)