Starting phenix.real_space_refine on Wed Jul 1 21:52:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kvv_62602/07_2026/9kvv_62602.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kvv_62602/07_2026/9kvv_62602.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kvv_62602/07_2026/9kvv_62602.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kvv_62602/07_2026/9kvv_62602.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kvv_62602/07_2026/9kvv_62602.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kvv_62602/07_2026/9kvv_62602.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 20 5.16 5 C 2056 2.51 5 N 495 2.21 5 O 559 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3131 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3115 Classifications: {'peptide': 410} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 16, 'TRANS': 393} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'BG6': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.01, per 1000 atoms: 0.32 Number of scatterers: 3131 At special positions: 0 Unit cell: (76.5, 56.95, 70.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 P 1 15.00 O 559 8.00 N 495 7.00 C 2056 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=0, symmetry=0 Time building additional restraints: 0.30 Conformation dependent library (CDL) restraints added in 126.6 milliseconds 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 740 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 0 sheets defined 88.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 6 through 34 removed outlier: 3.829A pdb=" N ARG A 10 " --> pdb=" O TYR A 6 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N PHE A 31 " --> pdb=" O ASN A 27 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N SER A 32 " --> pdb=" O ARG A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 40 removed outlier: 3.800A pdb=" N LEU A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 72 removed outlier: 3.913A pdb=" N PHE A 65 " --> pdb=" O ALA A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 95 removed outlier: 3.922A pdb=" N LEU A 79 " --> pdb=" O SER A 75 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA A 95 " --> pdb=" O ASN A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 114 Processing helix chain 'A' and resid 117 through 129 removed outlier: 4.282A pdb=" N CYS A 121 " --> pdb=" O GLY A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 163 removed outlier: 4.822A pdb=" N GLY A 135 " --> pdb=" O PRO A 131 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N THR A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SER A 144 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N MET A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASN A 146 " --> pdb=" O SER A 142 " (cutoff:3.500A) Proline residue: A 153 - end of helix removed outlier: 3.608A pdb=" N SER A 162 " --> pdb=" O ILE A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 187 removed outlier: 3.966A pdb=" N ALA A 170 " --> pdb=" O ARG A 166 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU A 171 " --> pdb=" O SER A 167 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER A 172 " --> pdb=" O THR A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 195 removed outlier: 3.904A pdb=" N VAL A 194 " --> pdb=" O GLU A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 222 removed outlier: 3.776A pdb=" N LEU A 222 " --> pdb=" O GLN A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 254 removed outlier: 3.896A pdb=" N TRP A 227 " --> pdb=" O SER A 223 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N GLN A 248 " --> pdb=" O THR A 244 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N PHE A 249 " --> pdb=" O ASP A 245 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU A 254 " --> pdb=" O PHE A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 291 Processing helix chain 'A' and resid 300 through 322 removed outlier: 3.859A pdb=" N VAL A 322 " --> pdb=" O PHE A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 357 removed outlier: 3.684A pdb=" N ILE A 331 " --> pdb=" O PRO A 327 " (cutoff:3.500A) Proline residue: A 345 - end of helix removed outlier: 3.560A pdb=" N GLY A 350 " --> pdb=" O ILE A 346 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA A 357 " --> pdb=" O ALA A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 360 No H-bonds generated for 'chain 'A' and resid 358 through 360' Processing helix chain 'A' and resid 361 through 380 removed outlier: 4.149A pdb=" N SER A 365 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N HIS A 366 " --> pdb=" O CYS A 362 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA A 380 " --> pdb=" O GLY A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 391 Processing helix chain 'A' and resid 392 through 414 removed outlier: 3.683A pdb=" N ALA A 396 " --> pdb=" O SER A 392 " (cutoff:3.500A) 253 hydrogen bonds defined for protein. 759 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.52 Time building geometry restraints manager: 0.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 938 1.34 - 1.46: 713 1.46 - 1.58: 1532 1.58 - 1.69: 1 1.69 - 1.81: 33 Bond restraints: 3217 Sorted by residual: bond pdb=" O6 BG6 A 501 " pdb=" P BG6 A 501 " ideal model delta sigma weight residual 1.723 1.644 0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" C3 BG6 A 501 " pdb=" O3 BG6 A 501 " ideal model delta sigma weight residual 1.408 1.474 -0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" C1 BG6 A 501 " pdb=" O5 BG6 A 501 " ideal model delta sigma weight residual 1.403 1.469 -0.066 2.00e-02 2.50e+03 1.07e+01 bond pdb=" C5 BG6 A 501 " pdb=" O5 BG6 A 501 " ideal model delta sigma weight residual 1.418 1.472 -0.054 2.00e-02 2.50e+03 7.24e+00 bond pdb=" C2 BG6 A 501 " pdb=" C3 BG6 A 501 " ideal model delta sigma weight residual 1.522 1.473 0.049 2.00e-02 2.50e+03 5.93e+00 ... (remaining 3212 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 4294 1.77 - 3.55: 70 3.55 - 5.32: 13 5.32 - 7.10: 5 7.10 - 8.87: 1 Bond angle restraints: 4383 Sorted by residual: angle pdb=" O2P BG6 A 501 " pdb=" P BG6 A 501 " pdb=" O6 BG6 A 501 " ideal model delta sigma weight residual 100.73 109.60 -8.87 3.00e+00 1.11e-01 8.74e+00 angle pdb=" N MET A 35 " pdb=" CA MET A 35 " pdb=" C MET A 35 " ideal model delta sigma weight residual 109.81 116.16 -6.35 2.21e+00 2.05e-01 8.26e+00 angle pdb=" N TRP A 118 " pdb=" CA TRP A 118 " pdb=" C TRP A 118 " ideal model delta sigma weight residual 109.81 115.45 -5.64 2.21e+00 2.05e-01 6.51e+00 angle pdb=" N PRO A 119 " pdb=" CA PRO A 119 " pdb=" C PRO A 119 " ideal model delta sigma weight residual 110.70 113.38 -2.68 1.22e+00 6.72e-01 4.82e+00 angle pdb=" O1P BG6 A 501 " pdb=" P BG6 A 501 " pdb=" O2P BG6 A 501 " ideal model delta sigma weight residual 115.54 109.38 6.16 3.00e+00 1.11e-01 4.22e+00 ... (remaining 4378 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.73: 1608 13.73 - 27.46: 147 27.46 - 41.18: 69 41.18 - 54.91: 18 54.91 - 68.64: 3 Dihedral angle restraints: 1845 sinusoidal: 682 harmonic: 1163 Sorted by residual: dihedral pdb=" CG ARG A 418 " pdb=" CD ARG A 418 " pdb=" NE ARG A 418 " pdb=" CZ ARG A 418 " ideal model delta sinusoidal sigma weight residual 180.00 136.55 43.45 2 1.50e+01 4.44e-03 1.01e+01 dihedral pdb=" CA LYS A 46 " pdb=" CB LYS A 46 " pdb=" CG LYS A 46 " pdb=" CD LYS A 46 " ideal model delta sinusoidal sigma weight residual -60.00 -115.35 55.35 3 1.50e+01 4.44e-03 9.34e+00 dihedral pdb=" CB MET A 288 " pdb=" CG MET A 288 " pdb=" SD MET A 288 " pdb=" CE MET A 288 " ideal model delta sinusoidal sigma weight residual -60.00 -112.64 52.64 3 1.50e+01 4.44e-03 9.13e+00 ... (remaining 1842 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 380 0.042 - 0.084: 99 0.084 - 0.126: 20 0.126 - 0.168: 1 0.168 - 0.210: 1 Chirality restraints: 501 Sorted by residual: chirality pdb=" CB VAL A 34 " pdb=" CA VAL A 34 " pdb=" CG1 VAL A 34 " pdb=" CG2 VAL A 34 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA TRP A 118 " pdb=" N TRP A 118 " pdb=" C TRP A 118 " pdb=" CB TRP A 118 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.66e-01 chirality pdb=" CA PRO A 131 " pdb=" N PRO A 131 " pdb=" C PRO A 131 " pdb=" CB PRO A 131 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.16e-01 ... (remaining 498 not shown) Planarity restraints: 535 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 36 " -0.007 2.00e-02 2.50e+03 1.49e-02 2.21e+00 pdb=" C PRO A 36 " 0.026 2.00e-02 2.50e+03 pdb=" O PRO A 36 " -0.010 2.00e-02 2.50e+03 pdb=" N SER A 37 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 298 " -0.024 5.00e-02 4.00e+02 3.65e-02 2.13e+00 pdb=" N PRO A 299 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 299 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 299 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 344 " -0.023 5.00e-02 4.00e+02 3.50e-02 1.96e+00 pdb=" N PRO A 345 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 345 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 345 " -0.020 5.00e-02 4.00e+02 ... (remaining 532 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 33 2.69 - 3.24: 3088 3.24 - 3.80: 5011 3.80 - 4.35: 5793 4.35 - 4.90: 10068 Nonbonded interactions: 23993 Sorted by model distance: nonbonded pdb=" OD1 ASN A 27 " pdb=" OG SER A 172 " model vdw 2.139 3.040 nonbonded pdb=" NH1 ARG A 423 " pdb=" O VAL A 424 " model vdw 2.317 3.120 nonbonded pdb=" N THR A 136 " pdb=" OD2 ASP A 285 " model vdw 2.326 3.120 nonbonded pdb=" O ILE A 140 " pdb=" OG1 THR A 143 " model vdw 2.330 3.040 nonbonded pdb=" OD1 ASN A 189 " pdb=" N GLU A 190 " model vdw 2.382 3.120 ... (remaining 23988 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.360 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.260 Find NCS groups from input model: 0.010 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 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 : 0.004 0.079 3217 Z= 0.199 Angle : 0.590 8.870 4383 Z= 0.296 Chirality : 0.038 0.210 501 Planarity : 0.004 0.036 535 Dihedral : 13.816 68.639 1105 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.00 (0.42), residues: 406 helix: 2.52 (0.28), residues: 334 sheet: None (None), residues: 0 loop : -0.68 (0.76), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 286 TYR 0.013 0.001 TYR A 265 PHE 0.018 0.001 PHE A 340 TRP 0.009 0.001 TRP A 118 HIS 0.000 0.000 HIS A 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.20 ( 3217) covalent geometry : angle 0.59014 / 0.30 ( 4383) hydrogen bonds : bond 0.09254 / 5.80 ( 253) hydrogen bonds : angle 3.88544 / 2.86 ( 759) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.067 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.0727 time to fit residues: 4.1906 Evaluate side-chains 44 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.0470 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 37 optimal weight: 0.3980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 ASN ** A 354 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 = 0.3979 r_free = 0.3979 target = 0.178467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.150654 restraints weight = 3893.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.151831 restraints weight = 2854.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.153022 restraints weight = 2479.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.153597 restraints weight = 2130.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.154508 restraints weight = 1951.874| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.0896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3217 Z= 0.138 Angle : 0.507 6.018 4383 Z= 0.267 Chirality : 0.038 0.149 501 Planarity : 0.004 0.035 535 Dihedral : 4.243 34.288 461 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.44 % Allowed : 6.40 % Favored : 91.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.96 (0.42), residues: 406 helix: 2.46 (0.28), residues: 339 sheet: None (None), residues: 0 loop : -0.76 (0.75), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 197 TYR 0.009 0.001 TYR A 24 PHE 0.018 0.001 PHE A 340 TRP 0.011 0.001 TRP A 118 HIS 0.000 0.000 HIS A 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 ( 3217) covalent geometry : angle 0.50700 / 0.27 ( 4383) hydrogen bonds : bond 0.05663 / 3.52 ( 253) hydrogen bonds : angle 3.55225 / 2.64 ( 759) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.112 Fit side-chains REVERT: A 219 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7131 (pt0) outliers start: 8 outliers final: 3 residues processed: 49 average time/residue: 0.0715 time to fit residues: 4.2588 Evaluate side-chains 47 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 417 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 ASN A 295 ASN ** A 354 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 = 0.3930 r_free = 0.3930 target = 0.173750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.145461 restraints weight = 3926.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.146111 restraints weight = 2991.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.147950 restraints weight = 2613.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.148469 restraints weight = 2333.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.148706 restraints weight = 2058.603| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3217 Z= 0.174 Angle : 0.527 5.935 4383 Z= 0.280 Chirality : 0.039 0.153 501 Planarity : 0.004 0.037 535 Dihedral : 4.254 34.132 461 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.83 % Allowed : 10.67 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.69 (0.41), residues: 406 helix: 2.27 (0.27), residues: 340 sheet: None (None), residues: 0 loop : -0.85 (0.73), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 423 TYR 0.008 0.001 TYR A 233 PHE 0.019 0.001 PHE A 340 TRP 0.010 0.001 TRP A 118 HIS 0.001 0.000 HIS A 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 ( 3217) covalent geometry : angle 0.52748 / 0.28 ( 4383) hydrogen bonds : bond 0.06573 / 4.15 ( 253) hydrogen bonds : angle 3.63300 / 2.68 ( 759) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.109 Fit side-chains REVERT: A 73 GLN cc_start: 0.8200 (tm-30) cc_final: 0.7389 (pt0) REVERT: A 219 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7104 (pt0) REVERT: A 288 MET cc_start: 0.8513 (tpt) cc_final: 0.8292 (tpp) REVERT: A 290 LYS cc_start: 0.7940 (ttpp) cc_final: 0.7334 (ttpt) outliers start: 6 outliers final: 3 residues processed: 43 average time/residue: 0.0660 time to fit residues: 3.5305 Evaluate side-chains 44 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 417 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 39 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 354 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 = 0.3756 r_free = 0.3756 target = 0.159853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.134369 restraints weight = 3695.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.134560 restraints weight = 3022.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.134751 restraints weight = 2856.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.136920 restraints weight = 2652.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.136926 restraints weight = 2301.306| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3217 Z= 0.178 Angle : 0.536 5.918 4383 Z= 0.283 Chirality : 0.038 0.156 501 Planarity : 0.005 0.037 535 Dihedral : 4.204 32.554 461 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.52 % Allowed : 14.94 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.73 (0.41), residues: 406 helix: 2.31 (0.28), residues: 340 sheet: None (None), residues: 0 loop : -0.96 (0.73), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 423 TYR 0.008 0.001 TYR A 233 PHE 0.019 0.001 PHE A 340 TRP 0.010 0.001 TRP A 118 HIS 0.001 0.000 HIS A 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 ( 3217) covalent geometry : angle 0.53577 / 0.28 ( 4383) hydrogen bonds : bond 0.06677 / 4.23 ( 253) hydrogen bonds : angle 3.57523 / 2.62 ( 759) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.068 Fit side-chains REVERT: A 73 GLN cc_start: 0.8174 (tm-30) cc_final: 0.7329 (pt0) REVERT: A 219 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.7006 (mt-10) REVERT: A 290 LYS cc_start: 0.8069 (ttpp) cc_final: 0.7358 (ttmt) outliers start: 5 outliers final: 3 residues processed: 41 average time/residue: 0.0563 time to fit residues: 2.7622 Evaluate side-chains 46 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 417 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 31 optimal weight: 0.1980 chunk 8 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 295 ASN ** A 354 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 = 0.3780 r_free = 0.3780 target = 0.161737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.136051 restraints weight = 3698.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.136272 restraints weight = 3007.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.136476 restraints weight = 2853.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.138589 restraints weight = 2631.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.138614 restraints weight = 2299.241| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3217 Z= 0.156 Angle : 0.520 6.262 4383 Z= 0.273 Chirality : 0.037 0.152 501 Planarity : 0.005 0.037 535 Dihedral : 4.121 31.069 461 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.13 % Allowed : 14.94 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.87 (0.42), residues: 406 helix: 2.40 (0.28), residues: 340 sheet: None (None), residues: 0 loop : -0.90 (0.72), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 197 TYR 0.007 0.001 TYR A 265 PHE 0.019 0.001 PHE A 340 TRP 0.010 0.001 TRP A 118 HIS 0.000 0.000 HIS A 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.16 ( 3217) covalent geometry : angle 0.52020 / 0.27 ( 4383) hydrogen bonds : bond 0.06288 / 3.95 ( 253) hydrogen bonds : angle 3.49363 / 2.55 ( 759) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.103 Fit side-chains REVERT: A 290 LYS cc_start: 0.8022 (ttpp) cc_final: 0.7341 (ttmt) outliers start: 7 outliers final: 6 residues processed: 43 average time/residue: 0.0424 time to fit residues: 2.2859 Evaluate side-chains 45 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 417 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 354 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 = 0.3770 r_free = 0.3770 target = 0.160739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.135292 restraints weight = 3689.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.135452 restraints weight = 2975.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.135651 restraints weight = 2843.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.137856 restraints weight = 2618.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.137879 restraints weight = 2250.368| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3217 Z= 0.167 Angle : 0.535 6.417 4383 Z= 0.279 Chirality : 0.038 0.153 501 Planarity : 0.005 0.037 535 Dihedral : 4.117 30.589 461 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.44 % Allowed : 15.85 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.82 (0.41), residues: 406 helix: 2.37 (0.28), residues: 340 sheet: None (None), residues: 0 loop : -0.90 (0.73), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 423 TYR 0.008 0.001 TYR A 233 PHE 0.020 0.001 PHE A 340 TRP 0.010 0.001 TRP A 138 HIS 0.001 0.000 HIS A 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 ( 3217) covalent geometry : angle 0.53451 / 0.28 ( 4383) hydrogen bonds : bond 0.06483 / 4.09 ( 253) hydrogen bonds : angle 3.53490 / 2.59 ( 759) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.127 Fit side-chains REVERT: A 290 LYS cc_start: 0.8047 (ttpp) cc_final: 0.7369 (ttmt) outliers start: 8 outliers final: 7 residues processed: 45 average time/residue: 0.0657 time to fit residues: 3.5881 Evaluate side-chains 47 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 417 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 7 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 4 optimal weight: 0.4980 chunk 14 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 354 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 = 0.3777 r_free = 0.3777 target = 0.161106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.135603 restraints weight = 3740.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.135865 restraints weight = 2981.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.136055 restraints weight = 2830.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.138255 restraints weight = 2608.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.138274 restraints weight = 2246.187| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3217 Z= 0.164 Angle : 0.526 6.738 4383 Z= 0.276 Chirality : 0.038 0.153 501 Planarity : 0.004 0.037 535 Dihedral : 4.088 29.752 461 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.74 % Allowed : 16.16 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.84 (0.41), residues: 406 helix: 2.38 (0.28), residues: 340 sheet: None (None), residues: 0 loop : -0.86 (0.73), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 197 TYR 0.007 0.001 TYR A 233 PHE 0.020 0.001 PHE A 340 TRP 0.010 0.001 TRP A 118 HIS 0.001 0.000 HIS A 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 ( 3217) covalent geometry : angle 0.52582 / 0.28 ( 4383) hydrogen bonds : bond 0.06430 / 4.05 ( 253) hydrogen bonds : angle 3.52503 / 2.58 ( 759) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.102 Fit side-chains REVERT: A 197 ARG cc_start: 0.7979 (tpt90) cc_final: 0.7639 (mmm160) REVERT: A 290 LYS cc_start: 0.8034 (ttpp) cc_final: 0.7313 (ttmt) outliers start: 9 outliers final: 6 residues processed: 46 average time/residue: 0.0703 time to fit residues: 3.9485 Evaluate side-chains 45 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 326 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 37 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 19 optimal weight: 0.2980 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 354 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 = 0.3770 r_free = 0.3770 target = 0.160545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.135059 restraints weight = 3803.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.135548 restraints weight = 2977.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.135727 restraints weight = 2822.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.138057 restraints weight = 2582.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.138168 restraints weight = 2143.524| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3217 Z= 0.163 Angle : 0.545 7.682 4383 Z= 0.280 Chirality : 0.038 0.152 501 Planarity : 0.004 0.037 535 Dihedral : 4.071 29.255 461 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.44 % Allowed : 17.07 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.83 (0.41), residues: 406 helix: 2.38 (0.28), residues: 340 sheet: None (None), residues: 0 loop : -0.90 (0.73), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 423 TYR 0.007 0.001 TYR A 233 PHE 0.020 0.001 PHE A 340 TRP 0.010 0.001 TRP A 138 HIS 0.001 0.000 HIS A 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 ( 3217) covalent geometry : angle 0.54528 / 0.28 ( 4383) hydrogen bonds : bond 0.06396 / 4.02 ( 253) hydrogen bonds : angle 3.51697 / 2.57 ( 759) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.065 Fit side-chains REVERT: A 290 LYS cc_start: 0.8025 (ttpp) cc_final: 0.7317 (ttmt) outliers start: 8 outliers final: 7 residues processed: 45 average time/residue: 0.0441 time to fit residues: 2.4745 Evaluate side-chains 47 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 417 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 9 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 354 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 = 0.3768 r_free = 0.3768 target = 0.160388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.135002 restraints weight = 3738.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.135353 restraints weight = 2962.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.135698 restraints weight = 2757.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.136235 restraints weight = 2581.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.136475 restraints weight = 2450.151| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3217 Z= 0.163 Angle : 0.555 8.405 4383 Z= 0.283 Chirality : 0.038 0.152 501 Planarity : 0.004 0.037 535 Dihedral : 4.072 28.723 461 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.74 % Allowed : 16.77 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.80 (0.41), residues: 406 helix: 2.36 (0.28), residues: 340 sheet: None (None), residues: 0 loop : -0.97 (0.72), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 197 TYR 0.007 0.001 TYR A 233 PHE 0.020 0.001 PHE A 340 TRP 0.010 0.001 TRP A 118 HIS 0.001 0.000 HIS A 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 ( 3217) covalent geometry : angle 0.55512 / 0.28 ( 4383) hydrogen bonds : bond 0.06409 / 4.03 ( 253) hydrogen bonds : angle 3.53831 / 2.59 ( 759) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.080 Fit side-chains REVERT: A 290 LYS cc_start: 0.7937 (ttpp) cc_final: 0.7295 (ttmt) outliers start: 9 outliers final: 9 residues processed: 42 average time/residue: 0.0623 time to fit residues: 3.2690 Evaluate side-chains 47 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 417 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 2 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 23 optimal weight: 0.2980 chunk 5 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 354 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 = 0.3770 r_free = 0.3770 target = 0.160499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.134774 restraints weight = 3634.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.135043 restraints weight = 2923.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.135258 restraints weight = 2755.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.137809 restraints weight = 2548.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.137923 restraints weight = 2101.889| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3217 Z= 0.161 Angle : 0.559 9.273 4383 Z= 0.284 Chirality : 0.038 0.151 501 Planarity : 0.004 0.037 535 Dihedral : 4.045 28.229 461 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.44 % Allowed : 16.77 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.81 (0.42), residues: 406 helix: 2.37 (0.28), residues: 340 sheet: None (None), residues: 0 loop : -0.94 (0.72), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 423 TYR 0.008 0.001 TYR A 265 PHE 0.020 0.001 PHE A 340 TRP 0.010 0.001 TRP A 138 HIS 0.001 0.000 HIS A 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 ( 3217) covalent geometry : angle 0.55893 / 0.28 ( 4383) hydrogen bonds : bond 0.06339 / 3.98 ( 253) hydrogen bonds : angle 3.52262 / 2.58 ( 759) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.142 Fit side-chains REVERT: A 197 ARG cc_start: 0.7932 (tpt90) cc_final: 0.7592 (mmm160) REVERT: A 290 LYS cc_start: 0.7985 (ttpp) cc_final: 0.7313 (ttmt) outliers start: 8 outliers final: 7 residues processed: 44 average time/residue: 0.0648 time to fit residues: 3.4957 Evaluate side-chains 47 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 417 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 354 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 = 0.3757 r_free = 0.3757 target = 0.159474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.133399 restraints weight = 3783.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.133548 restraints weight = 2919.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.133662 restraints weight = 2782.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.136224 restraints weight = 2591.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.136370 restraints weight = 2135.349| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3217 Z= 0.174 Angle : 0.564 8.160 4383 Z= 0.290 Chirality : 0.038 0.154 501 Planarity : 0.005 0.037 535 Dihedral : 4.083 28.535 461 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.74 % Allowed : 16.16 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.73 (0.41), residues: 406 helix: 2.31 (0.28), residues: 340 sheet: None (None), residues: 0 loop : -0.97 (0.72), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 197 TYR 0.007 0.001 TYR A 233 PHE 0.020 0.001 PHE A 340 TRP 0.010 0.001 TRP A 138 HIS 0.001 0.000 HIS A 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 ( 3217) covalent geometry : angle 0.56449 / 0.29 ( 4383) hydrogen bonds : bond 0.06635 / 4.18 ( 253) hydrogen bonds : angle 3.57894 / 2.62 ( 759) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 607.40 seconds wall clock time: 11 minutes 13.22 seconds (673.22 seconds total)