Starting phenix.real_space_refine on Fri Jul 25 03:23:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lq5_23481/07_2025/7lq5_23481.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lq5_23481/07_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_23481/07_2025/7lq5_23481.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lq5_23481/07_2025/7lq5_23481.map" model { file = "/net/cci-nas-00/data/ceres_data/7lq5_23481/07_2025/7lq5_23481.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lq5_23481/07_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-5711/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: 4.76, per 1000 atoms: 0.70 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: 2.26 Conformation dependent library (CDL) restraints added in 919.7 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: 0.55 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: 1.37 Time building geometry restraints manager: 2.56 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: 0.04 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: 4.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.500 Find NCS groups from input model: 0.110 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.740 ------------------------------------------------------------------------------- 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 : 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 Details of bonding type rmsd hydrogen bonds : bond 0.20723 ( 69) hydrogen bonds : angle 9.17489 ( 153) covalent geometry : bond 0.01327 ( 7188) covalent geometry : angle 1.30661 (10191) 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 : 0.702 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: 0.1975 time to fit residues: 28.4566 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 : 0.744 ------------------------------------------------------------------------------- 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: 1.9990 chunk 43 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.122242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.095539 restraints weight = 10019.922| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.73 r_work: 0.3239 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.352 7260 Z= 0.193 Angle : 0.939 12.279 10191 Z= 0.362 Chirality : 0.053 0.209 915 Planarity : 0.006 0.047 1251 Dihedral : 18.342 88.947 993 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % Rotamer: Outliers : 5.73 % Allowed : 24.43 % Favored : 69.83 % 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: -3.66 (0.27), residues: 768 helix: -3.87 (0.28), residues: 108 sheet: None (None), residues: 0 loop : -2.42 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 255 HIS 0.007 0.001 HIS B 91 PHE 0.015 0.002 PHE B 10 TYR 0.008 0.001 TYR C 109 ARG 0.006 0.001 ARG B 173 Details of bonding type rmsd hydrogen bonds : bond 0.03752 ( 69) hydrogen bonds : angle 6.93561 ( 153) covalent geometry : bond 0.00529 ( 7188) covalent geometry : angle 0.93928 (10191) Misc. bond : bond 0.10681 ( 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 115 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 77 time to evaluate : 0.651 Fit side-chains REVERT: A 15 ASP cc_start: 0.7567 (OUTLIER) cc_final: 0.6875 (t70) REVERT: A 239 TRP cc_start: 0.8461 (m100) cc_final: 0.8075 (m100) REVERT: B 15 ASP cc_start: 0.6932 (OUTLIER) cc_final: 0.6424 (t0) REVERT: B 128 SER cc_start: 0.8487 (m) cc_final: 0.8044 (p) REVERT: C 231 LYS cc_start: 0.7590 (mtmt) cc_final: 0.7317 (mmtm) REVERT: C 255 TRP cc_start: 0.7635 (OUTLIER) cc_final: 0.7271 (p90) outliers start: 38 outliers final: 25 residues processed: 108 average time/residue: 0.3600 time to fit residues: 56.9340 Evaluate side-chains 91 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 63 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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 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 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: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 34 optimal weight: 6.9990 chunk 18 optimal weight: 0.0270 chunk 12 optimal weight: 0.0030 chunk 70 optimal weight: 0.1980 chunk 52 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 overall best weight: 0.3248 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.125224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.099129 restraints weight = 9865.591| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.69 r_work: 0.3293 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.267 7260 Z= 0.142 Angle : 0.861 13.022 10191 Z= 0.324 Chirality : 0.049 0.160 915 Planarity : 0.005 0.046 1251 Dihedral : 18.085 87.275 993 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.07 % Favored : 88.93 % Rotamer: Outliers : 5.58 % Allowed : 28.36 % Favored : 66.06 % 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: -3.51 (0.28), residues: 768 helix: -3.32 (0.32), residues: 126 sheet: None (None), residues: 0 loop : -2.35 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 255 HIS 0.004 0.001 HIS B 91 PHE 0.010 0.001 PHE B 10 TYR 0.016 0.001 TYR C 109 ARG 0.003 0.001 ARG B 173 Details of bonding type rmsd hydrogen bonds : bond 0.03206 ( 69) hydrogen bonds : angle 6.45547 ( 153) covalent geometry : bond 0.00388 ( 7188) covalent geometry : angle 0.86073 (10191) Misc. bond : bond 0.08005 ( 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 127 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 90 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.7257 (OUTLIER) cc_final: 0.6522 (t70) REVERT: A 239 TRP cc_start: 0.8309 (m100) cc_final: 0.7879 (m100) REVERT: A 255 TRP cc_start: 0.7428 (OUTLIER) cc_final: 0.6337 (p90) REVERT: B 15 ASP cc_start: 0.6768 (OUTLIER) cc_final: 0.6401 (m-30) REVERT: B 110 CYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7853 (p) REVERT: B 128 SER cc_start: 0.8437 (m) cc_final: 0.7958 (p) REVERT: C 231 LYS cc_start: 0.7651 (mtmt) cc_final: 0.7285 (mmtm) outliers start: 37 outliers final: 26 residues processed: 117 average time/residue: 0.1841 time to fit residues: 29.8872 Evaluate side-chains 99 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 69 time to evaluate : 0.886 ------------------------------------------------------------------------------- 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 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 31 VAL 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: 3.9990 chunk 63 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 49 optimal weight: 0.0000 chunk 18 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 ASN ** C 8 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 = 0.3728 r_free = 0.3728 target = 0.122232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.096025 restraints weight = 10103.543| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.71 r_work: 0.3248 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.310 7260 Z= 0.193 Angle : 0.965 16.623 10191 Z= 0.345 Chirality : 0.050 0.134 915 Planarity : 0.005 0.043 1251 Dihedral : 18.086 88.749 991 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.89 % Favored : 87.11 % Rotamer: Outliers : 6.49 % Allowed : 30.17 % 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: -3.35 (0.28), residues: 768 helix: -3.40 (0.33), residues: 135 sheet: None (None), residues: 0 loop : -2.16 (0.24), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 255 HIS 0.005 0.001 HIS B 158 PHE 0.028 0.002 PHE C 10 TYR 0.013 0.001 TYR C 109 ARG 0.003 0.001 ARG B 173 Details of bonding type rmsd hydrogen bonds : bond 0.03438 ( 69) hydrogen bonds : angle 6.72170 ( 153) covalent geometry : bond 0.00525 ( 7188) covalent geometry : angle 0.96524 (10191) Misc. bond : bond 0.10033 ( 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 129 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 86 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.7609 (OUTLIER) cc_final: 0.6888 (t70) REVERT: A 236 ASP cc_start: 0.6953 (t0) cc_final: 0.6531 (t0) REVERT: A 239 TRP cc_start: 0.8415 (m100) cc_final: 0.7889 (m100) REVERT: A 255 TRP cc_start: 0.7568 (OUTLIER) cc_final: 0.6975 (p90) REVERT: B 15 ASP cc_start: 0.7108 (OUTLIER) cc_final: 0.6574 (t0) REVERT: B 110 CYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7957 (p) REVERT: B 128 SER cc_start: 0.8544 (m) cc_final: 0.8237 (t) REVERT: B 214 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8399 (tt) REVERT: C 64 LEU cc_start: 0.7912 (tp) cc_final: 0.7600 (tt) outliers start: 43 outliers final: 32 residues processed: 120 average time/residue: 0.1581 time to fit residues: 26.7930 Evaluate side-chains 112 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 75 time to evaluate : 0.834 ------------------------------------------------------------------------------- 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 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 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 1 optimal weight: 0.0050 chunk 44 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 46 optimal weight: 0.0970 chunk 4 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- 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** ** C 159 GLN ** 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 = 0.3754 r_free = 0.3754 target = 0.124197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.098239 restraints weight = 9945.216| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.68 r_work: 0.3280 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.295 7260 Z= 0.154 Angle : 0.895 15.195 10191 Z= 0.326 Chirality : 0.049 0.138 915 Planarity : 0.005 0.044 1251 Dihedral : 17.766 89.559 991 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.85 % Favored : 88.15 % Rotamer: Outliers : 7.09 % Allowed : 29.11 % Favored : 63.80 % 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: -2.95 (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 0.022 0.002 TRP B 255 HIS 0.004 0.001 HIS B 158 PHE 0.015 0.001 PHE C 10 TYR 0.013 0.001 TYR C 109 ARG 0.002 0.001 ARG B 85 Details of bonding type rmsd hydrogen bonds : bond 0.03177 ( 69) hydrogen bonds : angle 6.40516 ( 153) covalent geometry : bond 0.00426 ( 7188) covalent geometry : angle 0.89495 (10191) Misc. bond : bond 0.08142 ( 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 125 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 78 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 GLN cc_start: 0.8625 (mt0) cc_final: 0.8399 (mt0) REVERT: A 255 TRP cc_start: 0.7498 (OUTLIER) cc_final: 0.7103 (p90) REVERT: B 110 CYS cc_start: 0.8271 (OUTLIER) cc_final: 0.8006 (p) REVERT: B 128 SER cc_start: 0.8439 (m) cc_final: 0.8121 (t) REVERT: C 64 LEU cc_start: 0.7849 (tp) cc_final: 0.7478 (tt) outliers start: 47 outliers final: 36 residues processed: 114 average time/residue: 0.1539 time to fit residues: 24.3626 Evaluate side-chains 111 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 73 time to evaluate : 0.618 ------------------------------------------------------------------------------- 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 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 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 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: 2.9990 chunk 55 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 43 optimal weight: 0.0170 chunk 61 optimal weight: 6.9990 chunk 10 optimal weight: 0.3980 overall best weight: 1.6824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3663 r_free = 0.3663 target = 0.117503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.091562 restraints weight = 10308.267| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.62 r_work: 0.3206 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 0.517 7260 Z= 0.312 Angle : 1.203 18.268 10191 Z= 0.403 Chirality : 0.054 0.144 915 Planarity : 0.006 0.048 1251 Dihedral : 18.024 89.197 991 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.84 % Favored : 85.16 % Rotamer: Outliers : 8.45 % Allowed : 28.21 % 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: -3.19 (0.28), residues: 768 helix: -3.48 (0.34), residues: 108 sheet: None (None), residues: 0 loop : -2.09 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP B 255 HIS 0.008 0.002 HIS A 158 PHE 0.019 0.003 PHE C 10 TYR 0.011 0.002 TYR C 109 ARG 0.003 0.001 ARG A 173 Details of bonding type rmsd hydrogen bonds : bond 0.03906 ( 69) hydrogen bonds : angle 7.34547 ( 153) covalent geometry : bond 0.00821 ( 7188) covalent geometry : angle 1.20257 (10191) Misc. bond : bond 0.14817 ( 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 136 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 80 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.7631 (OUTLIER) cc_final: 0.7198 (t70) REVERT: A 239 TRP cc_start: 0.8385 (m100) cc_final: 0.8086 (m100) REVERT: A 255 TRP cc_start: 0.7508 (OUTLIER) cc_final: 0.7163 (p90) REVERT: B 110 CYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7873 (p) REVERT: B 128 SER cc_start: 0.8520 (m) cc_final: 0.8254 (t) REVERT: B 166 ASP cc_start: 0.8204 (m-30) cc_final: 0.7205 (t0) REVERT: B 214 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8383 (tt) REVERT: B 255 TRP cc_start: 0.7992 (OUTLIER) cc_final: 0.7100 (p90) REVERT: C 64 LEU cc_start: 0.8019 (tp) cc_final: 0.7760 (tt) outliers start: 56 outliers final: 40 residues processed: 127 average time/residue: 0.1394 time to fit residues: 25.7164 Evaluate side-chains 111 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 66 time to evaluate : 0.695 ------------------------------------------------------------------------------- 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 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 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 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 234 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 24 optimal weight: 0.0980 chunk 48 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 = 0.3673 r_free = 0.3673 target = 0.118165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.092294 restraints weight = 10140.039| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.59 r_work: 0.3189 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.386 7260 Z= 0.269 Angle : 1.104 17.338 10191 Z= 0.392 Chirality : 0.054 0.233 915 Planarity : 0.006 0.057 1251 Dihedral : 17.791 89.977 991 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.58 % Favored : 85.42 % Rotamer: Outliers : 8.30 % Allowed : 28.21 % Favored : 63.50 % 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: -3.21 (0.28), residues: 768 helix: -3.51 (0.33), residues: 108 sheet: None (None), residues: 0 loop : -2.10 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 255 HIS 0.006 0.001 HIS A 158 PHE 0.016 0.002 PHE C 18 TYR 0.015 0.002 TYR C 109 ARG 0.002 0.000 ARG A 173 Details of bonding type rmsd hydrogen bonds : bond 0.03722 ( 69) hydrogen bonds : angle 7.22005 ( 153) covalent geometry : bond 0.00717 ( 7188) covalent geometry : angle 1.10446 (10191) Misc. bond : bond 0.12212 ( 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: 55 poor density : 74 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.7684 (OUTLIER) cc_final: 0.7177 (t70) REVERT: A 173 ARG cc_start: 0.7914 (mtp85) cc_final: 0.7478 (mtp180) REVERT: B 110 CYS cc_start: 0.8246 (OUTLIER) cc_final: 0.8001 (p) REVERT: B 173 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.7237 (mtp180) REVERT: B 214 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8405 (tt) REVERT: B 255 TRP cc_start: 0.7875 (OUTLIER) cc_final: 0.7177 (p90) REVERT: C 64 LEU cc_start: 0.8048 (tp) cc_final: 0.7826 (tt) REVERT: C 130 SER cc_start: 0.8464 (m) cc_final: 0.8117 (t) outliers start: 55 outliers final: 40 residues processed: 120 average time/residue: 0.1385 time to fit residues: 23.7368 Evaluate side-chains 110 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 65 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 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 173 ARG 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 252 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 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 220 ASP Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 248 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 43 optimal weight: 0.0770 chunk 27 optimal weight: 2.9990 chunk 31 optimal weight: 0.0870 chunk 33 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 8 optimal weight: 0.4980 chunk 32 optimal weight: 0.0870 chunk 53 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 overall best weight: 0.2694 ------------------------------------------------------------------------------- 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 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 = 0.3760 r_free = 0.3760 target = 0.124564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.098294 restraints weight = 10074.742| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.71 r_work: 0.3286 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.271 7260 Z= 0.145 Angle : 0.916 14.357 10191 Z= 0.344 Chirality : 0.050 0.195 915 Planarity : 0.006 0.055 1251 Dihedral : 17.152 87.305 989 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.28 % Favored : 86.72 % Rotamer: Outliers : 6.33 % Allowed : 30.02 % Favored : 63.65 % 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: -2.99 (0.29), residues: 768 helix: -3.06 (0.34), residues: 126 sheet: None (None), residues: 0 loop : -1.94 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 255 HIS 0.004 0.001 HIS C 241 PHE 0.013 0.002 PHE A 256 TYR 0.023 0.001 TYR C 109 ARG 0.002 0.000 ARG B 139 Details of bonding type rmsd hydrogen bonds : bond 0.03101 ( 69) hydrogen bonds : angle 6.65398 ( 153) covalent geometry : bond 0.00385 ( 7188) covalent geometry : angle 0.91581 (10191) Misc. bond : bond 0.07127 ( 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 123 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 81 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ARG cc_start: 0.7697 (mtp85) cc_final: 0.7361 (mtt90) REVERT: A 219 LYS cc_start: 0.8054 (tptt) cc_final: 0.6992 (mptt) REVERT: B 110 CYS cc_start: 0.8320 (OUTLIER) cc_final: 0.8076 (p) REVERT: B 255 TRP cc_start: 0.7697 (OUTLIER) cc_final: 0.7229 (p90) REVERT: C 64 LEU cc_start: 0.7861 (tp) cc_final: 0.7521 (tt) REVERT: C 130 SER cc_start: 0.8189 (m) cc_final: 0.7809 (t) outliers start: 42 outliers final: 34 residues processed: 112 average time/residue: 0.1661 time to fit residues: 25.8118 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 : 0.698 ------------------------------------------------------------------------------- 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 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 A residue 256 PHE 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 147 ASN Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 208 CYS 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 208 CYS 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: 0.6980 chunk 11 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 49 optimal weight: 0.0470 chunk 3 optimal weight: 0.9980 chunk 42 optimal weight: 0.0770 chunk 57 optimal weight: 3.9990 chunk 68 optimal weight: 0.0870 chunk 70 optimal weight: 0.0980 chunk 30 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 overall best weight: 0.1814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN B 245 ASN B 249 GLN C 245 ASN C 249 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.127665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.101844 restraints weight = 9992.561| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.70 r_work: 0.3350 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.226 7260 Z= 0.138 Angle : 0.911 13.840 10191 Z= 0.339 Chirality : 0.049 0.173 915 Planarity : 0.006 0.052 1251 Dihedral : 16.911 89.671 989 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.76 % Favored : 87.24 % Rotamer: Outliers : 4.98 % Allowed : 31.22 % Favored : 63.80 % 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: -2.53 (0.30), residues: 768 helix: -2.33 (0.45), residues: 99 sheet: None (None), residues: 0 loop : -1.75 (0.25), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 255 HIS 0.003 0.001 HIS C 241 PHE 0.014 0.001 PHE A 256 TYR 0.021 0.001 TYR C 109 ARG 0.002 0.000 ARG C 173 Details of bonding type rmsd hydrogen bonds : bond 0.03010 ( 69) hydrogen bonds : angle 6.32987 ( 153) covalent geometry : bond 0.00360 ( 7188) covalent geometry : angle 0.91055 (10191) Misc. bond : bond 0.05988 ( 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 106 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 73 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7904 (mp0) cc_final: 0.7679 (mp0) REVERT: A 111 HIS cc_start: 0.8085 (OUTLIER) cc_final: 0.7551 (t-90) REVERT: A 155 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7031 (mm-30) REVERT: A 173 ARG cc_start: 0.7518 (mtp85) cc_final: 0.7059 (mtp180) REVERT: A 219 LYS cc_start: 0.8007 (tptt) cc_final: 0.7029 (mptt) REVERT: B 110 CYS cc_start: 0.8329 (OUTLIER) cc_final: 0.8099 (p) REVERT: B 255 TRP cc_start: 0.7468 (OUTLIER) cc_final: 0.7142 (p90) REVERT: C 64 LEU cc_start: 0.7730 (tp) cc_final: 0.7438 (tt) outliers start: 33 outliers final: 25 residues processed: 98 average time/residue: 0.1486 time to fit residues: 20.6992 Evaluate side-chains 98 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 70 time to evaluate : 0.627 ------------------------------------------------------------------------------- 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 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 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 84 PHE 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 147 ASN Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 208 CYS Chi-restraints excluded: chain B residue 255 TRP Chi-restraints excluded: chain C residue 87 CYS Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 110 CYS 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 30 optimal weight: 3.9990 chunk 42 optimal weight: 0.1980 chunk 12 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 45 optimal weight: 0.0870 chunk 8 optimal weight: 0.0060 chunk 63 optimal weight: 0.9980 chunk 46 optimal weight: 0.0370 chunk 20 optimal weight: 0.9990 overall best weight: 0.2652 ------------------------------------------------------------------------------- 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 245 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 = 0.3807 r_free = 0.3807 target = 0.127824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.102065 restraints weight = 10141.682| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.72 r_work: 0.3343 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.198 7260 Z= 0.137 Angle : 0.912 14.284 10191 Z= 0.335 Chirality : 0.049 0.162 915 Planarity : 0.006 0.054 1251 Dihedral : 16.900 88.208 989 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.37 % Favored : 87.63 % Rotamer: Outliers : 4.68 % Allowed : 31.07 % 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: -2.39 (0.30), residues: 768 helix: -2.07 (0.47), residues: 99 sheet: None (None), residues: 0 loop : -1.67 (0.25), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 255 HIS 0.003 0.001 HIS C 252 PHE 0.014 0.001 PHE A 256 TYR 0.022 0.001 TYR C 109 ARG 0.002 0.000 ARG A 139 Details of bonding type rmsd hydrogen bonds : bond 0.02948 ( 69) hydrogen bonds : angle 6.31954 ( 153) covalent geometry : bond 0.00366 ( 7188) covalent geometry : angle 0.91214 (10191) Misc. bond : bond 0.05935 ( 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 105 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 74 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7659 (mp0) cc_final: 0.7149 (mp0) REVERT: A 111 HIS cc_start: 0.7960 (OUTLIER) cc_final: 0.7396 (t-90) REVERT: A 219 LYS cc_start: 0.8002 (tptt) cc_final: 0.7090 (mptt) REVERT: B 110 CYS cc_start: 0.8276 (OUTLIER) cc_final: 0.8046 (p) REVERT: B 255 TRP cc_start: 0.7402 (OUTLIER) cc_final: 0.7065 (p90) REVERT: C 64 LEU cc_start: 0.7624 (tp) cc_final: 0.7312 (tt) outliers start: 31 outliers final: 24 residues processed: 98 average time/residue: 0.1567 time to fit residues: 22.0929 Evaluate side-chains 96 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 69 time to evaluate : 0.687 ------------------------------------------------------------------------------- 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 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 208 CYS 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 255 TRP Chi-restraints excluded: chain C residue 87 CYS Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 110 CYS 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 29 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 45 optimal weight: 0.0970 chunk 41 optimal weight: 0.0970 chunk 71 optimal weight: 7.9990 chunk 63 optimal weight: 0.4980 chunk 48 optimal weight: 0.2980 chunk 55 optimal weight: 8.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.3576 ------------------------------------------------------------------------------- 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 245 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 = 0.3799 r_free = 0.3799 target = 0.127112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.101463 restraints weight = 10005.379| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.69 r_work: 0.3336 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.204 7260 Z= 0.143 Angle : 0.922 14.720 10191 Z= 0.339 Chirality : 0.049 0.153 915 Planarity : 0.006 0.052 1251 Dihedral : 16.911 88.405 989 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.76 % Favored : 87.24 % Rotamer: Outliers : 4.98 % Allowed : 30.77 % 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: -2.31 (0.30), residues: 768 helix: -1.97 (0.49), residues: 99 sheet: None (None), residues: 0 loop : -1.63 (0.25), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 255 HIS 0.003 0.001 HIS C 252 PHE 0.014 0.001 PHE A 256 TYR 0.021 0.001 TYR C 109 ARG 0.002 0.000 ARG A 173 Details of bonding type rmsd hydrogen bonds : bond 0.03006 ( 69) hydrogen bonds : angle 6.39381 ( 153) covalent geometry : bond 0.00381 ( 7188) covalent geometry : angle 0.92189 (10191) Misc. bond : bond 0.06380 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4144.18 seconds wall clock time: 73 minutes 38.57 seconds (4418.57 seconds total)