Starting phenix.real_space_refine on Wed Feb 12 01:44:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lq5_23481/02_2025/7lq5_23481.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lq5_23481/02_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_23481/02_2025/7lq5_23481.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lq5_23481/02_2025/7lq5_23481.map" model { file = "/net/cci-nas-00/data/ceres_data/7lq5_23481/02_2025/7lq5_23481.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lq5_23481/02_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-5592/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: 4.73, per 1000 atoms: 0.69 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: 2.35 Conformation dependent library (CDL) restraints added in 947.2 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: 0.66 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: 1.47 Time building geometry restraints manager: 2.59 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: 7.010 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: 0.150 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.720 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.119 7188 Z= 0.826 Angle : 1.307 7.053 10191 Z= 0.644 Chirality : 0.068 0.267 915 Planarity : 0.009 0.044 1251 Dihedral : 19.666 83.396 2268 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 27.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.89 % Favored : 87.11 % Rotamer: Outliers : 0.45 % Allowed : 30.32 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.95 (0.24), residues: 768 helix: -4.81 (0.13), residues: 126 sheet: None (None), residues: 0 loop : -3.31 (0.21), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.007 TRP A 239 HIS 0.022 0.005 HIS C 97 PHE 0.020 0.005 PHE B 176 TYR 0.015 0.006 TYR C 109 ARG 0.008 0.003 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 107 time to evaluate : 0.664 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: 0.2026 time to fit residues: 29.5298 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 : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 TRP Chi-restraints excluded: chain B residue 255 TRP Chi-restraints excluded: chain C residue 255 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 19 optimal weight: 10.0000 chunk 38 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 HIS B 199 ASN ** B 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 HIS C 199 ASN C 245 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.122806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.096342 restraints weight = 9984.470| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.71 r_work: 0.3245 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 7188 Z= 0.302 Angle : 0.929 12.159 10191 Z= 0.358 Chirality : 0.052 0.209 915 Planarity : 0.006 0.047 1251 Dihedral : 18.304 88.872 993 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.55 % Favored : 89.45 % Rotamer: Outliers : 5.88 % Allowed : 25.04 % Favored : 69.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (0.27), residues: 768 helix: -3.85 (0.28), residues: 108 sheet: None (None), residues: 0 loop : -2.39 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 255 HIS 0.007 0.001 HIS B 91 PHE 0.016 0.002 PHE B 10 TYR 0.009 0.001 TYR C 109 ARG 0.004 0.001 ARG B 173 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 80 time to evaluate : 0.658 Fit side-chains REVERT: A 15 ASP cc_start: 0.7563 (OUTLIER) cc_final: 0.6866 (t70) REVERT: A 239 TRP cc_start: 0.8452 (m100) cc_final: 0.8047 (m100) REVERT: B 15 ASP cc_start: 0.6946 (OUTLIER) cc_final: 0.6429 (t0) REVERT: B 128 SER cc_start: 0.8461 (m) cc_final: 0.8020 (p) REVERT: C 37 VAL cc_start: 0.8762 (m) cc_final: 0.8553 (t) REVERT: C 231 LYS cc_start: 0.7595 (mtmt) cc_final: 0.7339 (mmtm) REVERT: C 255 TRP cc_start: 0.7620 (OUTLIER) cc_final: 0.7310 (p90) outliers start: 39 outliers final: 24 residues processed: 111 average time/residue: 0.1647 time to fit residues: 25.2006 Evaluate side-chains 94 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 67 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 255 TRP Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 255 TRP Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 191 ASN Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 255 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 43 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.0040 chunk 23 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 12 optimal weight: 0.1980 chunk 70 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- 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 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 = 0.3747 r_free = 0.3747 target = 0.123715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.097679 restraints weight = 9930.274| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.67 r_work: 0.3273 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 7188 Z= 0.262 Angle : 0.895 14.100 10191 Z= 0.331 Chirality : 0.050 0.159 915 Planarity : 0.006 0.045 1251 Dihedral : 18.158 87.835 993 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.98 % Favored : 88.02 % Rotamer: Outliers : 6.33 % Allowed : 28.81 % Favored : 64.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (0.28), residues: 768 helix: -3.62 (0.29), residues: 144 sheet: None (None), residues: 0 loop : -2.31 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 255 HIS 0.004 0.001 HIS B 91 PHE 0.010 0.001 PHE B 10 TYR 0.015 0.001 TYR C 109 ARG 0.004 0.001 ARG A 173 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 83 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.7431 (OUTLIER) cc_final: 0.6680 (t70) REVERT: A 236 ASP cc_start: 0.6990 (t0) cc_final: 0.6698 (t0) REVERT: A 239 TRP cc_start: 0.8430 (m100) cc_final: 0.7995 (m100) REVERT: A 255 TRP cc_start: 0.7548 (OUTLIER) cc_final: 0.6367 (p90) REVERT: B 110 CYS cc_start: 0.8253 (OUTLIER) cc_final: 0.8004 (p) REVERT: B 128 SER cc_start: 0.8533 (m) cc_final: 0.8067 (p) REVERT: C 64 LEU cc_start: 0.7870 (tp) cc_final: 0.7561 (tt) REVERT: C 231 LYS cc_start: 0.7662 (mtmt) cc_final: 0.7252 (mmtm) outliers start: 42 outliers final: 31 residues processed: 115 average time/residue: 0.1670 time to fit residues: 26.8099 Evaluate side-chains 105 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 71 time to evaluate : 0.737 ------------------------------------------------------------------------------- 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 72 VAL Chi-restraints excluded: chain A residue 96 HIS Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 208 CYS Chi-restraints excluded: chain A residue 255 TRP Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 0 optimal weight: 4.9990 chunk 5 optimal weight: 0.0470 chunk 63 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 overall best weight: 0.8882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 ASN ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.121360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.094944 restraints weight = 10112.197| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.74 r_work: 0.3226 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 7188 Z= 0.321 Angle : 0.970 16.334 10191 Z= 0.343 Chirality : 0.051 0.136 915 Planarity : 0.006 0.042 1251 Dihedral : 18.120 88.296 991 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.02 % Favored : 86.98 % Rotamer: Outliers : 6.94 % Allowed : 29.71 % 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: -3.54 (0.28), residues: 768 helix: -3.49 (0.30), residues: 144 sheet: None (None), residues: 0 loop : -2.28 (0.24), residues: 624 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 0.029 0.002 PHE C 10 TYR 0.014 0.002 TYR C 109 ARG 0.002 0.001 ARG A 173 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 87 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.7657 (OUTLIER) cc_final: 0.6937 (t70) REVERT: A 236 ASP cc_start: 0.7048 (t0) cc_final: 0.6813 (t0) REVERT: A 239 TRP cc_start: 0.8419 (m100) cc_final: 0.7943 (m100) REVERT: A 255 TRP cc_start: 0.7560 (OUTLIER) cc_final: 0.6969 (p90) REVERT: B 110 CYS cc_start: 0.8286 (OUTLIER) cc_final: 0.8026 (p) REVERT: B 128 SER cc_start: 0.8554 (m) cc_final: 0.8248 (t) REVERT: B 214 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8404 (tt) REVERT: C 64 LEU cc_start: 0.7954 (tp) cc_final: 0.7621 (tt) outliers start: 46 outliers final: 35 residues processed: 122 average time/residue: 0.1611 time to fit residues: 27.8683 Evaluate side-chains 114 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 75 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 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 191 ASN 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 234 LEU 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: 1.9990 chunk 44 optimal weight: 7.9990 chunk 55 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 28 optimal weight: 0.0770 chunk 35 optimal weight: 3.9990 overall best weight: 1.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 ASN ** B 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 ASN ** C 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 ASN ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.118072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.092106 restraints weight = 10182.479| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.61 r_work: 0.3181 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 7188 Z= 0.424 Angle : 1.125 17.936 10191 Z= 0.382 Chirality : 0.053 0.144 915 Planarity : 0.006 0.045 1251 Dihedral : 18.135 89.635 991 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.19 % Favored : 85.81 % Rotamer: Outliers : 9.05 % Allowed : 27.75 % Favored : 63.20 % 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: -3.20 (0.28), residues: 768 helix: -3.44 (0.36), residues: 108 sheet: None (None), residues: 0 loop : -2.11 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 255 HIS 0.008 0.001 HIS B 158 PHE 0.017 0.002 PHE C 10 TYR 0.013 0.002 TYR C 109 ARG 0.005 0.001 ARG A 173 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 77 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.7700 (OUTLIER) cc_final: 0.7189 (t70) REVERT: A 239 TRP cc_start: 0.8494 (m100) cc_final: 0.8185 (m100) REVERT: A 255 TRP cc_start: 0.7458 (OUTLIER) cc_final: 0.7144 (p90) REVERT: B 110 CYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7928 (p) REVERT: B 128 SER cc_start: 0.8429 (m) cc_final: 0.8199 (t) REVERT: B 173 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.7268 (mtp180) REVERT: B 214 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8415 (tt) REVERT: B 255 TRP cc_start: 0.7903 (OUTLIER) cc_final: 0.7059 (p90) REVERT: C 64 LEU cc_start: 0.8043 (tp) cc_final: 0.7811 (tt) outliers start: 60 outliers final: 41 residues processed: 123 average time/residue: 0.1517 time to fit residues: 26.4548 Evaluate side-chains 113 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 66 time to evaluate : 0.718 ------------------------------------------------------------------------------- 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 29 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 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 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 199 ASN Chi-restraints excluded: chain C residue 208 CYS Chi-restraints excluded: chain C residue 234 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 ASN ** B 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 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 = 0.3694 r_free = 0.3694 target = 0.119489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.092635 restraints weight = 10263.949| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.73 r_work: 0.3194 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 7188 Z= 0.361 Angle : 1.036 17.122 10191 Z= 0.369 Chirality : 0.052 0.259 915 Planarity : 0.006 0.055 1251 Dihedral : 17.771 89.252 991 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.06 % Favored : 85.94 % Rotamer: Outliers : 8.90 % Allowed : 28.05 % Favored : 63.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.49 (0.27), residues: 768 helix: -3.55 (0.32), residues: 126 sheet: None (None), residues: 0 loop : -2.28 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 255 HIS 0.005 0.001 HIS B 158 PHE 0.015 0.002 PHE C 10 TYR 0.013 0.002 TYR C 109 ARG 0.002 0.000 ARG A 85 *********************** 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 133 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 74 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 ASP cc_start: 0.7014 (t0) cc_final: 0.6634 (t0) REVERT: A 239 TRP cc_start: 0.8427 (m100) cc_final: 0.8062 (m100) REVERT: B 28 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7987 (mm-30) REVERT: B 110 CYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7961 (p) REVERT: B 128 SER cc_start: 0.8439 (m) cc_final: 0.8235 (t) REVERT: B 173 ARG cc_start: 0.7755 (mtp85) cc_final: 0.7233 (mtp180) REVERT: B 214 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8423 (tt) REVERT: B 255 TRP cc_start: 0.7890 (OUTLIER) cc_final: 0.7196 (p90) REVERT: C 64 LEU cc_start: 0.8043 (tp) cc_final: 0.7808 (tt) outliers start: 59 outliers final: 41 residues processed: 124 average time/residue: 0.1511 time to fit residues: 26.4791 Evaluate side-chains 108 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 64 time to evaluate : 0.686 ------------------------------------------------------------------------------- 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 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 54 ILE 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 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 24 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 ASN ** B 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 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 = 0.3707 r_free = 0.3707 target = 0.120253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.093806 restraints weight = 10121.715| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.71 r_work: 0.3218 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 7188 Z= 0.329 Angle : 1.007 17.049 10191 Z= 0.360 Chirality : 0.051 0.226 915 Planarity : 0.006 0.049 1251 Dihedral : 17.475 89.534 989 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.10 % Favored : 84.90 % Rotamer: Outliers : 7.54 % Allowed : 28.51 % Favored : 63.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.28), residues: 768 helix: -3.32 (0.33), residues: 126 sheet: None (None), residues: 0 loop : -2.02 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 255 HIS 0.004 0.001 HIS B 91 PHE 0.011 0.002 PHE B 10 TYR 0.016 0.002 TYR C 109 ARG 0.002 0.000 ARG A 173 *********************** 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 120 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 70 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 ASP cc_start: 0.7038 (t0) cc_final: 0.6731 (t0) REVERT: A 239 TRP cc_start: 0.8408 (m100) cc_final: 0.8028 (m100) REVERT: B 110 CYS cc_start: 0.8245 (OUTLIER) cc_final: 0.8002 (p) REVERT: B 128 SER cc_start: 0.8481 (m) cc_final: 0.8258 (t) REVERT: B 173 ARG cc_start: 0.7776 (mtp85) cc_final: 0.7227 (mtp180) REVERT: B 214 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8408 (tt) REVERT: B 255 TRP cc_start: 0.7797 (OUTLIER) cc_final: 0.7226 (p90) REVERT: C 64 LEU cc_start: 0.7949 (tp) cc_final: 0.7682 (tt) REVERT: C 130 SER cc_start: 0.8434 (m) cc_final: 0.8045 (t) REVERT: C 227 LEU cc_start: 0.7696 (mm) cc_final: 0.7461 (mp) outliers start: 50 outliers final: 40 residues processed: 112 average time/residue: 0.1522 time to fit residues: 24.0611 Evaluate side-chains 109 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 66 time to evaluate : 0.673 ------------------------------------------------------------------------------- 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 22 THR Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 147 ASN Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 191 ASN Chi-restraints excluded: chain B residue 208 CYS Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 248 CYS Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 255 TRP Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 87 CYS Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain C residue 191 ASN Chi-restraints excluded: chain C residue 208 CYS Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 248 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 0.0170 chunk 70 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 chunk 32 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 ASN ** B 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.121934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.095893 restraints weight = 10159.979| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.68 r_work: 0.3248 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 7188 Z= 0.267 Angle : 0.944 15.851 10191 Z= 0.342 Chirality : 0.050 0.191 915 Planarity : 0.006 0.047 1251 Dihedral : 17.261 87.783 989 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.93 % Favored : 86.07 % Rotamer: Outliers : 6.79 % Allowed : 28.51 % Favored : 64.71 % 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: -3.04 (0.29), residues: 768 helix: -3.23 (0.33), residues: 126 sheet: None (None), residues: 0 loop : -1.95 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 255 HIS 0.004 0.001 HIS B 158 PHE 0.013 0.001 PHE A 256 TYR 0.016 0.001 TYR C 109 ARG 0.003 0.000 ARG A 173 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 77 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 ASP cc_start: 0.7031 (t0) cc_final: 0.6707 (t0) REVERT: A 239 TRP cc_start: 0.8356 (m100) cc_final: 0.7946 (m100) REVERT: B 110 CYS cc_start: 0.8325 (OUTLIER) cc_final: 0.8096 (p) REVERT: B 128 SER cc_start: 0.8455 (m) cc_final: 0.8239 (t) REVERT: B 255 TRP cc_start: 0.7766 (OUTLIER) cc_final: 0.7222 (p90) REVERT: C 64 LEU cc_start: 0.7835 (tp) cc_final: 0.7521 (tt) REVERT: C 130 SER cc_start: 0.8373 (m) cc_final: 0.7971 (t) REVERT: C 227 LEU cc_start: 0.7746 (mm) cc_final: 0.7533 (mp) outliers start: 45 outliers final: 39 residues processed: 112 average time/residue: 0.1510 time to fit residues: 23.9795 Evaluate side-chains 113 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 72 time to evaluate : 0.686 ------------------------------------------------------------------------------- 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 22 THR Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 147 ASN Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 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 103 VAL Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain C residue 191 ASN Chi-restraints excluded: chain C residue 208 CYS Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 248 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 23 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN A 249 GLN B 86 ASN ** B 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 ASN C 199 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.119821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.093888 restraints weight = 10233.676| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.65 r_work: 0.3218 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 7188 Z= 0.359 Angle : 1.049 17.516 10191 Z= 0.366 Chirality : 0.052 0.174 915 Planarity : 0.006 0.046 1251 Dihedral : 17.438 89.406 989 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.62 % Favored : 84.38 % Rotamer: Outliers : 7.69 % Allowed : 27.30 % 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 (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: -3.09 (0.28), residues: 768 helix: -3.31 (0.32), residues: 126 sheet: None (None), residues: 0 loop : -1.97 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 255 HIS 0.006 0.001 HIS C 158 PHE 0.017 0.002 PHE A 256 TYR 0.015 0.002 TYR C 109 ARG 0.002 0.000 ARG C 85 *********************** 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 124 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 73 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 ASP cc_start: 0.7012 (t0) cc_final: 0.6768 (t0) REVERT: A 239 TRP cc_start: 0.8382 (m100) cc_final: 0.8026 (m100) REVERT: B 110 CYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7992 (p) REVERT: B 214 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8407 (tt) REVERT: B 255 TRP cc_start: 0.7789 (OUTLIER) cc_final: 0.7200 (p90) REVERT: C 64 LEU cc_start: 0.7951 (tp) cc_final: 0.7686 (tt) REVERT: C 130 SER cc_start: 0.8457 (m) cc_final: 0.8066 (t) outliers start: 51 outliers final: 42 residues processed: 112 average time/residue: 0.1401 time to fit residues: 22.6201 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 : 0.666 ------------------------------------------------------------------------------- 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 22 THR Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 147 ASN Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 191 ASN Chi-restraints excluded: chain B residue 208 CYS Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 248 CYS Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 255 TRP Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 87 CYS Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain C residue 191 ASN Chi-restraints excluded: chain C residue 208 CYS Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 248 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 30 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 ASN ** B 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.120814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.094826 restraints weight = 10306.544| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.67 r_work: 0.3238 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 7188 Z= 0.312 Angle : 1.003 16.390 10191 Z= 0.362 Chirality : 0.051 0.174 915 Planarity : 0.006 0.056 1251 Dihedral : 17.221 89.143 989 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.45 % Favored : 85.55 % Rotamer: Outliers : 7.09 % Allowed : 28.36 % 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 (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: -3.00 (0.29), residues: 768 helix: -3.15 (0.34), residues: 126 sheet: None (None), residues: 0 loop : -1.93 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 255 HIS 0.004 0.001 HIS A 158 PHE 0.015 0.002 PHE A 256 TYR 0.023 0.002 TYR C 109 ARG 0.002 0.000 ARG A 85 ********************** 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 119 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 72 time to evaluate : 0.718 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: 0.8071 (tptt) cc_final: 0.6778 (mptt) REVERT: A 236 ASP cc_start: 0.7049 (t0) cc_final: 0.6775 (t0) REVERT: A 239 TRP cc_start: 0.8348 (m100) cc_final: 0.7924 (m100) REVERT: B 110 CYS cc_start: 0.8278 (OUTLIER) cc_final: 0.8038 (p) REVERT: B 255 TRP cc_start: 0.7736 (OUTLIER) cc_final: 0.7220 (p90) REVERT: C 64 LEU cc_start: 0.7965 (tp) cc_final: 0.7686 (tt) REVERT: C 130 SER cc_start: 0.8401 (m) cc_final: 0.8051 (t) outliers start: 47 outliers final: 42 residues processed: 108 average time/residue: 0.1456 time to fit residues: 22.6725 Evaluate side-chains 112 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 68 time to evaluate : 0.639 ------------------------------------------------------------------------------- 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 22 THR Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 54 ILE 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 199 ASN Chi-restraints excluded: chain B residue 208 CYS Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 248 CYS Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 255 TRP Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 87 CYS Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain C residue 191 ASN Chi-restraints excluded: chain C residue 208 CYS Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 248 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 29 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 73 optimal weight: 0.1980 chunk 45 optimal weight: 0.5980 chunk 41 optimal weight: 0.2980 chunk 71 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 chunk 48 optimal weight: 0.3980 chunk 55 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 HIS ** B 245 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 = 0.3760 r_free = 0.3760 target = 0.123929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.098433 restraints weight = 10033.871| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.62 r_work: 0.3297 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7188 Z= 0.247 Angle : 0.942 14.832 10191 Z= 0.349 Chirality : 0.049 0.172 915 Planarity : 0.006 0.055 1251 Dihedral : 17.000 86.521 989 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.32 % Favored : 85.68 % Rotamer: Outliers : 5.58 % Allowed : 29.71 % Favored : 64.71 % 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: -2.66 (0.30), residues: 768 helix: -2.80 (0.40), residues: 117 sheet: None (None), residues: 0 loop : -1.73 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 255 HIS 0.003 0.001 HIS B 158 PHE 0.013 0.001 PHE C 256 TYR 0.022 0.001 TYR C 109 ARG 0.001 0.000 ARG A 85 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3499.43 seconds wall clock time: 63 minutes 9.91 seconds (3789.91 seconds total)