Starting phenix.real_space_refine on Tue Mar 3 16:18:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lq5_23481/03_2026/7lq5_23481.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lq5_23481/03_2026/7lq5_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_2026/7lq5_23481.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lq5_23481/03_2026/7lq5_23481.map" model { file = "/net/cci-nas-00/data/ceres_data/7lq5_23481/03_2026/7lq5_23481.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lq5_23481/03_2026/7lq5_23481.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: B, C Time building chain proxies: 1.09, per 1000 atoms: 0.16 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: 0.62 Conformation dependent library (CDL) restraints added in 141.3 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: 0.17 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: 0.84 Time building geometry restraints manager: 0.78 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.450 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 5.870 Find NCS groups from input model: 0.050 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:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.530 ------------------------------------------------------------------------------- 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 : 0.019 0.435 7260 Z= 1.181 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 : 26.33 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.008 0.003 ARG B 139 TYR 0.015 0.006 TYR C 109 PHE 0.020 0.005 PHE B 176 TRP 0.026 0.007 TRP A 239 HIS 0.022 0.005 HIS C 97 Details of bonding type rmsd covalent geometry : bond 0.01327 ( 7188) covalent geometry : angle 1.30661 (10191) hydrogen bonds : bond 0.20723 ( 69) hydrogen bonds : angle 9.17489 ( 153) Misc. bond : bond 0.14220 ( 72) *********************** 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 : 0.163 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: 0.0717 time to fit residues: 10.5147 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 : 0.164 ------------------------------------------------------------------------------- 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 49 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.0000 chunk 74 optimal weight: 2.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 ASN ** B 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 ASN C 245 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.123665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.097106 restraints weight = 10067.000| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.73 r_work: 0.3263 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.298 7260 Z= 0.171 Angle : 0.911 11.675 10191 Z= 0.355 Chirality : 0.052 0.209 915 Planarity : 0.006 0.048 1251 Dihedral : 18.234 87.939 993 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.16 % Favored : 89.84 % Rotamer: Outliers : 6.03 % Allowed : 24.59 % Favored : 69.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.60 (0.27), residues: 768 helix: -3.82 (0.28), residues: 108 sheet: None (None), residues: 0 loop : -2.38 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 173 TYR 0.009 0.001 TYR C 109 PHE 0.016 0.002 PHE B 10 TRP 0.024 0.002 TRP C 255 HIS 0.007 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00471 ( 7188) covalent geometry : angle 0.91078 (10191) hydrogen bonds : bond 0.03623 ( 69) hydrogen bonds : angle 6.77009 ( 153) Misc. bond : bond 0.09195 ( 72) *********************** 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 124 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 84 time to evaluate : 0.157 Fit side-chains REVERT: A 15 ASP cc_start: 0.7464 (OUTLIER) cc_final: 0.6717 (t70) REVERT: A 239 TRP cc_start: 0.8437 (m100) cc_final: 0.8032 (m100) REVERT: B 15 ASP cc_start: 0.6908 (OUTLIER) cc_final: 0.6373 (t0) REVERT: B 128 SER cc_start: 0.8458 (m) cc_final: 0.7998 (p) REVERT: C 37 VAL cc_start: 0.8761 (m) cc_final: 0.8561 (t) REVERT: C 231 LYS cc_start: 0.7557 (mtmt) cc_final: 0.7309 (mmtm) REVERT: C 255 TRP cc_start: 0.7566 (OUTLIER) cc_final: 0.7265 (p90) outliers start: 40 outliers final: 24 residues processed: 116 average time/residue: 0.0641 time to fit residues: 10.3967 Evaluate side-chains 97 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 70 time to evaluate : 0.173 ------------------------------------------------------------------------------- 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 68 optimal weight: 0.0050 chunk 58 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 23 optimal weight: 0.0470 chunk 0 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 45 optimal weight: 0.0030 chunk 38 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 overall best weight: 0.2902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 ASN C 199 ASN ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.125829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.099785 restraints weight = 9920.486| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.69 r_work: 0.3301 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.278 7260 Z= 0.142 Angle : 0.863 13.240 10191 Z= 0.324 Chirality : 0.049 0.156 915 Planarity : 0.005 0.046 1251 Dihedral : 17.993 87.265 993 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.81 % Favored : 89.19 % Rotamer: Outliers : 4.68 % Allowed : 28.51 % Favored : 66.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.28 (0.28), residues: 768 helix: -3.30 (0.34), residues: 117 sheet: None (None), residues: 0 loop : -2.17 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 173 TYR 0.015 0.001 TYR C 109 PHE 0.010 0.001 PHE B 10 TRP 0.022 0.002 TRP B 255 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 7188) covalent geometry : angle 0.86262 (10191) hydrogen bonds : bond 0.03188 ( 69) hydrogen bonds : angle 6.37370 ( 153) Misc. bond : bond 0.07872 ( 72) *********************** 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 119 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 88 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 LYS cc_start: 0.8629 (mppt) cc_final: 0.8407 (mttt) REVERT: A 236 ASP cc_start: 0.6793 (t0) cc_final: 0.6576 (t0) REVERT: A 239 TRP cc_start: 0.8323 (m100) cc_final: 0.7870 (m100) REVERT: A 255 TRP cc_start: 0.7399 (OUTLIER) cc_final: 0.6290 (p90) REVERT: B 110 CYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7810 (p) REVERT: B 128 SER cc_start: 0.8419 (m) cc_final: 0.7938 (p) REVERT: C 64 LEU cc_start: 0.7760 (tp) cc_final: 0.7442 (tt) REVERT: C 231 LYS cc_start: 0.7696 (mtmt) cc_final: 0.7328 (mmtm) outliers start: 31 outliers final: 22 residues processed: 110 average time/residue: 0.0660 time to fit residues: 10.2063 Evaluate side-chains 94 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 70 time to evaluate : 0.229 ------------------------------------------------------------------------------- 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 72 VAL 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 154 CYS Chi-restraints excluded: chain A residue 208 CYS Chi-restraints excluded: chain A residue 255 TRP Chi-restraints excluded: chain B residue 31 VAL 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 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 208 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 55 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 21 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 ASN C 245 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.122127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.095922 restraints weight = 10073.219| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.71 r_work: 0.3245 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.438 7260 Z= 0.191 Angle : 0.960 16.759 10191 Z= 0.341 Chirality : 0.050 0.134 915 Planarity : 0.005 0.043 1251 Dihedral : 17.947 88.575 991 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % Rotamer: Outliers : 6.49 % Allowed : 29.41 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.30 (0.29), residues: 768 helix: -3.37 (0.32), residues: 135 sheet: None (None), residues: 0 loop : -2.12 (0.25), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 173 TYR 0.013 0.001 TYR C 109 PHE 0.013 0.002 PHE B 18 TRP 0.023 0.002 TRP B 255 HIS 0.004 0.001 HIS A 158 Details of bonding type rmsd covalent geometry : bond 0.00516 ( 7188) covalent geometry : angle 0.96017 (10191) hydrogen bonds : bond 0.03483 ( 69) hydrogen bonds : angle 6.64657 ( 153) Misc. bond : bond 0.10646 ( 72) *********************** 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 128 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 85 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.7641 (OUTLIER) cc_final: 0.6905 (t70) REVERT: A 236 ASP cc_start: 0.7084 (t0) cc_final: 0.6809 (t0) REVERT: A 239 TRP cc_start: 0.8391 (m100) cc_final: 0.7870 (m100) REVERT: A 255 TRP cc_start: 0.7543 (OUTLIER) cc_final: 0.6952 (p90) REVERT: B 110 CYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7961 (p) REVERT: B 128 SER cc_start: 0.8539 (m) cc_final: 0.8237 (t) REVERT: B 214 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8397 (tt) REVERT: C 64 LEU cc_start: 0.7846 (tp) cc_final: 0.7502 (tt) outliers start: 43 outliers final: 32 residues processed: 119 average time/residue: 0.0630 time to fit residues: 10.6715 Evaluate side-chains 107 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 71 time to evaluate : 0.160 ------------------------------------------------------------------------------- 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 196 THR Chi-restraints excluded: chain A residue 208 CYS Chi-restraints excluded: chain A residue 255 TRP 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 52 optimal weight: 5.9990 chunk 23 optimal weight: 0.0470 chunk 29 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 43 optimal weight: 0.4980 chunk 62 optimal weight: 4.9990 overall best weight: 1.0882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.119974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.093842 restraints weight = 10192.056| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.65 r_work: 0.3219 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.389 7260 Z= 0.225 Angle : 1.019 16.778 10191 Z= 0.357 Chirality : 0.052 0.143 915 Planarity : 0.006 0.044 1251 Dihedral : 18.040 89.577 991 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.15 % Favored : 86.85 % Rotamer: Outliers : 8.14 % Allowed : 27.90 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.35 (0.28), residues: 768 helix: -3.29 (0.35), residues: 126 sheet: None (None), residues: 0 loop : -2.21 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 173 TYR 0.012 0.002 TYR C 109 PHE 0.023 0.002 PHE C 10 TRP 0.025 0.002 TRP B 255 HIS 0.006 0.001 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00611 ( 7188) covalent geometry : angle 1.01888 (10191) hydrogen bonds : bond 0.03649 ( 69) hydrogen bonds : angle 6.87392 ( 153) Misc. bond : bond 0.11517 ( 72) *********************** 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 142 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 88 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ARG cc_start: 0.7977 (mtp85) cc_final: 0.7212 (mtp180) REVERT: A 236 ASP cc_start: 0.7079 (t0) cc_final: 0.6831 (t0) REVERT: A 239 TRP cc_start: 0.8481 (m100) cc_final: 0.8106 (m100) REVERT: A 255 TRP cc_start: 0.7382 (OUTLIER) cc_final: 0.7082 (p90) REVERT: B 110 CYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7948 (p) REVERT: B 128 SER cc_start: 0.8450 (m) cc_final: 0.8193 (t) REVERT: B 214 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8389 (tt) REVERT: B 255 TRP cc_start: 0.7799 (OUTLIER) cc_final: 0.7070 (p90) REVERT: C 64 LEU cc_start: 0.7900 (tp) cc_final: 0.7616 (tt) outliers start: 54 outliers final: 39 residues processed: 128 average time/residue: 0.0669 time to fit residues: 12.0742 Evaluate side-chains 113 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 70 time to evaluate : 0.200 ------------------------------------------------------------------------------- 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 234 LEU Chi-restraints excluded: chain A residue 255 TRP 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 42 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 51 optimal weight: 0.2980 chunk 52 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 ASN C 117 ASN ** C 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.116614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.090523 restraints weight = 10315.455| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.62 r_work: 0.3161 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 0.512 7260 Z= 0.324 Angle : 1.216 18.148 10191 Z= 0.412 Chirality : 0.055 0.228 915 Planarity : 0.006 0.056 1251 Dihedral : 18.047 89.059 991 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.54 % Favored : 83.46 % Rotamer: Outliers : 8.45 % Allowed : 27.60 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.30 (0.28), residues: 768 helix: -3.49 (0.34), residues: 108 sheet: None (None), residues: 0 loop : -2.18 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 173 TYR 0.011 0.002 TYR C 109 PHE 0.017 0.003 PHE C 10 TRP 0.027 0.003 TRP B 255 HIS 0.007 0.002 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00850 ( 7188) covalent geometry : angle 1.21625 (10191) hydrogen bonds : bond 0.04025 ( 69) hydrogen bonds : angle 7.43545 ( 153) Misc. bond : bond 0.14868 ( 72) *********************** 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 126 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 70 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 TRP cc_start: 0.8487 (m100) cc_final: 0.8256 (m100) REVERT: A 255 TRP cc_start: 0.7530 (OUTLIER) cc_final: 0.7305 (p90) REVERT: B 110 CYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7841 (p) REVERT: B 128 SER cc_start: 0.8502 (m) cc_final: 0.8297 (t) REVERT: B 214 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8408 (tt) REVERT: B 255 TRP cc_start: 0.7971 (OUTLIER) cc_final: 0.7116 (p90) REVERT: C 64 LEU cc_start: 0.8148 (tp) cc_final: 0.7887 (tt) outliers start: 56 outliers final: 41 residues processed: 117 average time/residue: 0.0592 time to fit residues: 10.2726 Evaluate side-chains 108 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 63 time to evaluate : 0.235 ------------------------------------------------------------------------------- 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 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 245 ASN 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 50 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 46 optimal weight: 0.4980 chunk 22 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 0.0570 chunk 62 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 16 optimal weight: 0.0370 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 ASN ** 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 = 0.3737 r_free = 0.3737 target = 0.122812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.096239 restraints weight = 10048.887| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.72 r_work: 0.3256 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.296 7260 Z= 0.154 Angle : 0.928 15.105 10191 Z= 0.348 Chirality : 0.050 0.231 915 Planarity : 0.006 0.052 1251 Dihedral : 17.374 87.197 991 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % Rotamer: Outliers : 6.49 % Allowed : 29.56 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.03 (0.29), residues: 768 helix: -3.07 (0.39), residues: 108 sheet: None (None), residues: 0 loop : -2.03 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 85 TYR 0.017 0.001 TYR C 109 PHE 0.011 0.002 PHE C 10 TRP 0.023 0.002 TRP A 255 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 7188) covalent geometry : angle 0.92776 (10191) hydrogen bonds : bond 0.03222 ( 69) hydrogen bonds : angle 6.58584 ( 153) Misc. bond : bond 0.08068 ( 72) *********************** 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 129 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 86 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ARG cc_start: 0.7761 (mtp85) cc_final: 0.7309 (mtp180) REVERT: A 236 ASP cc_start: 0.7122 (t0) cc_final: 0.6748 (t0) REVERT: A 239 TRP cc_start: 0.8424 (m100) cc_final: 0.8072 (m100) REVERT: A 249 GLN cc_start: 0.8635 (mt0) cc_final: 0.8427 (mt0) REVERT: B 110 CYS cc_start: 0.8268 (OUTLIER) cc_final: 0.8011 (p) REVERT: B 128 SER cc_start: 0.8411 (m) cc_final: 0.8205 (t) REVERT: B 237 LEU cc_start: 0.7936 (tt) cc_final: 0.7689 (tp) REVERT: B 255 TRP cc_start: 0.7763 (OUTLIER) cc_final: 0.7209 (p90) REVERT: C 64 LEU cc_start: 0.7956 (tp) cc_final: 0.7691 (tt) REVERT: C 130 SER cc_start: 0.8389 (m) cc_final: 0.8016 (t) outliers start: 43 outliers final: 33 residues processed: 119 average time/residue: 0.0642 time to fit residues: 11.1089 Evaluate side-chains 112 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 77 time to evaluate : 0.154 ------------------------------------------------------------------------------- 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 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 31 VAL Chi-restraints excluded: chain B residue 56 THR 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 154 CYS 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 74 optimal weight: 0.0270 chunk 36 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 70 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 73 optimal weight: 0.3980 chunk 26 optimal weight: 0.5980 chunk 46 optimal weight: 10.0000 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3716 r_free = 0.3716 target = 0.120954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.094858 restraints weight = 10285.207| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.66 r_work: 0.3234 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.285 7260 Z= 0.191 Angle : 1.003 16.756 10191 Z= 0.362 Chirality : 0.051 0.186 915 Planarity : 0.006 0.048 1251 Dihedral : 17.388 89.831 989 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.71 % Favored : 85.29 % Rotamer: Outliers : 6.79 % Allowed : 28.21 % Favored : 65.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.01 (0.29), residues: 768 helix: -3.20 (0.36), residues: 108 sheet: None (None), residues: 0 loop : -1.99 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 173 TYR 0.015 0.001 TYR C 109 PHE 0.013 0.002 PHE C 10 TRP 0.024 0.002 TRP B 255 HIS 0.003 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00519 ( 7188) covalent geometry : angle 1.00300 (10191) hydrogen bonds : bond 0.03458 ( 69) hydrogen bonds : angle 6.87450 ( 153) Misc. bond : bond 0.09386 ( 72) *********************** 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 118 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 73 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 LYS cc_start: 0.8038 (tptt) cc_final: 0.6819 (mptt) REVERT: A 236 ASP cc_start: 0.7065 (t0) cc_final: 0.6736 (t0) REVERT: A 239 TRP cc_start: 0.8376 (m100) cc_final: 0.7975 (m100) REVERT: B 110 CYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7996 (p) REVERT: B 128 SER cc_start: 0.8496 (m) cc_final: 0.8274 (t) REVERT: B 237 LEU cc_start: 0.7925 (tt) cc_final: 0.7581 (tp) REVERT: B 255 TRP cc_start: 0.7795 (OUTLIER) cc_final: 0.7263 (p90) REVERT: C 64 LEU cc_start: 0.7910 (tp) cc_final: 0.7628 (tt) outliers start: 45 outliers final: 39 residues processed: 108 average time/residue: 0.0624 time to fit residues: 9.8530 Evaluate side-chains 109 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 68 time to evaluate : 0.232 ------------------------------------------------------------------------------- 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 A residue 256 PHE 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 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 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 234 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 31 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 71 optimal weight: 8.9990 chunk 37 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 74 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN ** B 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3723 r_free = 0.3723 target = 0.121628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.095769 restraints weight = 10191.371| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.64 r_work: 0.3247 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.273 7260 Z= 0.185 Angle : 0.989 16.270 10191 Z= 0.362 Chirality : 0.051 0.179 915 Planarity : 0.006 0.048 1251 Dihedral : 17.244 88.982 989 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.58 % Favored : 85.42 % Rotamer: Outliers : 7.09 % Allowed : 28.05 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.03 (0.29), residues: 768 helix: -3.02 (0.34), residues: 126 sheet: None (None), residues: 0 loop : -1.99 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 173 TYR 0.016 0.001 TYR C 109 PHE 0.017 0.002 PHE A 256 TRP 0.024 0.002 TRP B 255 HIS 0.004 0.001 HIS B 252 Details of bonding type rmsd covalent geometry : bond 0.00503 ( 7188) covalent geometry : angle 0.98853 (10191) hydrogen bonds : bond 0.03487 ( 69) hydrogen bonds : angle 6.84690 ( 153) Misc. bond : bond 0.09035 ( 72) *********************** 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 122 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 75 time to evaluate : 0.142 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: 0.8049 (tptt) cc_final: 0.6860 (mptt) REVERT: A 236 ASP cc_start: 0.7070 (t0) cc_final: 0.6688 (t0) REVERT: A 239 TRP cc_start: 0.8334 (m100) cc_final: 0.7918 (m100) REVERT: B 110 CYS cc_start: 0.8255 (OUTLIER) cc_final: 0.8015 (p) REVERT: B 237 LEU cc_start: 0.7966 (tt) cc_final: 0.7619 (tp) REVERT: B 255 TRP cc_start: 0.7738 (OUTLIER) cc_final: 0.7213 (p90) REVERT: C 64 LEU cc_start: 0.7884 (tp) cc_final: 0.7600 (tt) REVERT: C 130 SER cc_start: 0.8434 (m) cc_final: 0.8071 (t) outliers start: 47 outliers final: 42 residues processed: 112 average time/residue: 0.0602 time to fit residues: 9.6487 Evaluate side-chains 113 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 69 time to evaluate : 0.172 ------------------------------------------------------------------------------- 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 A residue 214 LEU Chi-restraints excluded: chain A residue 256 PHE 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 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 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 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 39 optimal weight: 0.5980 chunk 70 optimal weight: 0.4980 chunk 8 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 13 optimal weight: 0.3980 chunk 5 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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** ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3733 r_free = 0.3733 target = 0.122278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.096508 restraints weight = 10080.889| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.63 r_work: 0.3265 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.264 7260 Z= 0.173 Angle : 0.976 16.014 10191 Z= 0.361 Chirality : 0.050 0.172 915 Planarity : 0.006 0.047 1251 Dihedral : 17.188 88.418 989 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.93 % Favored : 86.07 % Rotamer: Outliers : 6.64 % Allowed : 28.81 % Favored : 64.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.89 (0.29), residues: 768 helix: -2.79 (0.37), residues: 126 sheet: None (None), residues: 0 loop : -1.92 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 173 TYR 0.022 0.001 TYR C 109 PHE 0.016 0.002 PHE A 256 TRP 0.023 0.002 TRP B 255 HIS 0.004 0.001 HIS B 252 Details of bonding type rmsd covalent geometry : bond 0.00469 ( 7188) covalent geometry : angle 0.97592 (10191) hydrogen bonds : bond 0.03333 ( 69) hydrogen bonds : angle 6.72482 ( 153) Misc. bond : bond 0.08338 ( 72) ********************** 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 113 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 69 time to evaluate : 0.277 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: 0.8054 (tptt) cc_final: 0.6873 (mptt) REVERT: A 236 ASP cc_start: 0.6979 (t0) cc_final: 0.6629 (t0) REVERT: A 239 TRP cc_start: 0.8312 (m100) cc_final: 0.7924 (m100) REVERT: B 110 CYS cc_start: 0.8286 (OUTLIER) cc_final: 0.8044 (p) REVERT: B 237 LEU cc_start: 0.7943 (tt) cc_final: 0.7585 (tp) REVERT: B 255 TRP cc_start: 0.7690 (OUTLIER) cc_final: 0.7244 (p90) REVERT: C 64 LEU cc_start: 0.7902 (tp) cc_final: 0.7603 (tt) REVERT: C 130 SER cc_start: 0.8400 (m) cc_final: 0.8020 (t) outliers start: 44 outliers final: 38 residues processed: 106 average time/residue: 0.0620 time to fit residues: 9.7055 Evaluate side-chains 106 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 66 time to evaluate : 0.219 ------------------------------------------------------------------------------- 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 A residue 214 LEU 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 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 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 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 191 ASN Chi-restraints excluded: chain C residue 208 CYS 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 65 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 68 optimal weight: 0.0370 chunk 71 optimal weight: 2.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 HIS ** B 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3740 r_free = 0.3740 target = 0.122923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.097143 restraints weight = 10119.307| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.64 r_work: 0.3270 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.253 7260 Z= 0.168 Angle : 0.966 15.776 10191 Z= 0.358 Chirality : 0.050 0.171 915 Planarity : 0.006 0.047 1251 Dihedral : 17.205 87.775 989 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.67 % Favored : 86.33 % Rotamer: Outliers : 5.58 % Allowed : 30.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.66 (0.30), residues: 768 helix: -2.49 (0.42), residues: 117 sheet: None (None), residues: 0 loop : -1.80 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 173 TYR 0.021 0.001 TYR C 109 PHE 0.012 0.001 PHE C 256 TRP 0.023 0.002 TRP B 255 HIS 0.004 0.001 HIS B 252 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 7188) covalent geometry : angle 0.96622 (10191) hydrogen bonds : bond 0.03196 ( 69) hydrogen bonds : angle 6.67693 ( 153) Misc. bond : bond 0.08003 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1873.28 seconds wall clock time: 32 minutes 44.43 seconds (1964.43 seconds total)