Starting phenix.real_space_refine on Wed Jul 1 23:06:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8b6z_15893/07_2026/8b6z_15893.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b6z_15893/07_2026/8b6z_15893.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8b6z_15893/07_2026/8b6z_15893.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b6z_15893/07_2026/8b6z_15893.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8b6z_15893/07_2026/8b6z_15893.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8b6z_15893/07_2026/8b6z_15893.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8b6z_15893/07_2026/8b6z_15893.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b6z_15893/07_2026/8b6z_15893.map" } resolution = 2.9 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= 0.001 sd= 0.007 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 8 5.49 5 S 16 5.16 5 C 2240 2.51 5 N 624 2.21 5 O 693 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s 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: 3581 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3406 Classifications: {'peptide': 442} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 415} Chain: "B" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 175 Classifications: {'RNA': 8} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna3p': 7} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N GLY A 50 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY A 50 " occ=0.00 Time building chain proxies: 1.05, per 1000 atoms: 0.29 Number of scatterers: 3581 At special positions: 0 Unit cell: (65.934, 93.906, 67.932, 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 16 16.00 P 8 15.00 O 693 8.00 N 624 7.00 C 2240 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: 0.36 Conformation dependent library (CDL) restraints added in 142.7 milliseconds 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 806 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 5 sheets defined 25.1% alpha, 33.3% beta 1 base pairs and 4 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 19 through 32 Processing helix chain 'A' and resid 35 through 50 Processing helix chain 'A' and resid 57 through 66 Processing helix chain 'A' and resid 97 through 105 Processing helix chain 'A' and resid 121 through 127 removed outlier: 3.703A pdb=" N ILE A 127 " --> pdb=" O PHE A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 144 Processing helix chain 'A' and resid 154 through 158 removed outlier: 3.836A pdb=" N SER A 157 " --> pdb=" O LYS A 154 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR A 158 " --> pdb=" O MET A 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 154 through 158' Processing helix chain 'A' and resid 163 through 182 removed outlier: 3.601A pdb=" N TYR A 177 " --> pdb=" O GLU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 188 Processing helix chain 'A' and resid 227 through 234 removed outlier: 3.715A pdb=" N ALA A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 421 Processing sheet with id=AA1, first strand: chain 'A' and resid 79 through 81 removed outlier: 6.557A pdb=" N ILE A 8 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ILE A 90 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ILE A 10 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N CYS A 111 " --> pdb=" O HIS A 7 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ASN A 9 " --> pdb=" O CYS A 111 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N VAL A 113 " --> pdb=" O ASN A 9 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL A 11 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILE A 115 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ILE A 13 " --> pdb=" O ILE A 115 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N ALA A 117 " --> pdb=" O ILE A 13 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL A 191 " --> pdb=" O VAL A 150 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 214 through 216 Processing sheet with id=AA3, first strand: chain 'A' and resid 247 through 249 removed outlier: 6.659A pdb=" N ASN A 311 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N VAL A 292 " --> pdb=" O GLY A 309 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N GLY A 309 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N MET A 294 " --> pdb=" O ASN A 307 " (cutoff:3.500A) removed outlier: 9.275A pdb=" N ASN A 307 " --> pdb=" O MET A 294 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N THR A 261 " --> pdb=" O VAL A 312 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 247 through 249 Processing sheet with id=AA5, first strand: chain 'A' and resid 386 through 389 removed outlier: 6.610A pdb=" N ALA A 373 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N VAL A 405 " --> pdb=" O ALA A 373 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LEU A 375 " --> pdb=" O GLU A 403 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N GLU A 403 " --> pdb=" O LEU A 375 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ALA A 338 " --> pdb=" O PRO A 406 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN A 339 " --> pdb=" O GLU A 442 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLN A 343 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ILE A 438 " --> pdb=" O GLN A 343 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ILE A 345 " --> pdb=" O GLY A 436 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N GLY A 436 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N THR A 432 " --> pdb=" O ASP A 428 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ASP A 428 " --> pdb=" O THR A 432 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL A 360 " --> pdb=" O ARG A 427 " (cutoff:3.500A) 136 hydrogen bonds defined for protein. 366 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2 hydrogen bonds 4 hydrogen bond angles 0 basepair planarities 1 basepair parallelities 4 stacking parallelities Total time for adding SS restraints: 0.59 Time building geometry restraints manager: 0.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1126 1.34 - 1.46: 522 1.46 - 1.57: 1984 1.57 - 1.69: 15 1.69 - 1.81: 26 Bond restraints: 3673 Sorted by residual: bond pdb=" C ILE A 235 " pdb=" N LEU A 236 " ideal model delta sigma weight residual 1.327 1.339 -0.012 1.39e-02 5.18e+03 7.88e-01 bond pdb=" N VAL A 152 " pdb=" CA VAL A 152 " ideal model delta sigma weight residual 1.465 1.476 -0.011 1.38e-02 5.25e+03 5.94e-01 bond pdb=" CA GLY A 351 " pdb=" C GLY A 351 " ideal model delta sigma weight residual 1.514 1.505 0.010 1.41e-02 5.03e+03 4.55e-01 bond pdb=" CA HIS A 364 " pdb=" CB HIS A 364 " ideal model delta sigma weight residual 1.530 1.541 -0.011 1.69e-02 3.50e+03 4.23e-01 bond pdb=" C LYS A 165 " pdb=" O LYS A 165 " ideal model delta sigma weight residual 1.236 1.228 0.008 1.26e-02 6.30e+03 4.09e-01 ... (remaining 3668 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 4915 1.47 - 2.93: 71 2.93 - 4.40: 20 4.40 - 5.86: 1 5.86 - 7.33: 1 Bond angle restraints: 5008 Sorted by residual: angle pdb=" N GLY A 182 " pdb=" CA GLY A 182 " pdb=" C GLY A 182 " ideal model delta sigma weight residual 113.18 120.51 -7.33 2.37e+00 1.78e-01 9.56e+00 angle pdb=" N SER A 157 " pdb=" CA SER A 157 " pdb=" C SER A 157 " ideal model delta sigma weight residual 112.88 115.26 -2.38 1.29e+00 6.01e-01 3.40e+00 angle pdb=" CB LYS A 172 " pdb=" CG LYS A 172 " pdb=" CD LYS A 172 " ideal model delta sigma weight residual 111.30 115.15 -3.85 2.30e+00 1.89e-01 2.80e+00 angle pdb=" CA GLY A 182 " pdb=" C GLY A 182 " pdb=" N TYR A 183 " ideal model delta sigma weight residual 116.69 119.99 -3.30 2.04e+00 2.40e-01 2.62e+00 angle pdb=" N ASN A 200 " pdb=" CA ASN A 200 " pdb=" CB ASN A 200 " ideal model delta sigma weight residual 113.15 110.58 2.57 1.63e+00 3.76e-01 2.48e+00 ... (remaining 5003 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.78: 2053 13.78 - 27.56: 106 27.56 - 41.33: 33 41.33 - 55.11: 14 55.11 - 68.89: 4 Dihedral angle restraints: 2210 sinusoidal: 951 harmonic: 1259 Sorted by residual: dihedral pdb=" CA VAL A 152 " pdb=" C VAL A 152 " pdb=" N ASN A 153 " pdb=" CA ASN A 153 " ideal model delta harmonic sigma weight residual -180.00 -161.01 -18.99 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA PRO A 160 " pdb=" C PRO A 160 " pdb=" N ALA A 161 " pdb=" CA ALA A 161 " ideal model delta harmonic sigma weight residual -180.00 -162.08 -17.92 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA ILE A 178 " pdb=" C ILE A 178 " pdb=" N LYS A 179 " pdb=" CA LYS A 179 " ideal model delta harmonic sigma weight residual 180.00 162.10 17.90 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 2207 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 309 0.025 - 0.050: 155 0.050 - 0.075: 37 0.075 - 0.100: 31 0.100 - 0.125: 37 Chirality restraints: 569 Sorted by residual: chirality pdb=" CA ILE A 401 " pdb=" N ILE A 401 " pdb=" C ILE A 401 " pdb=" CB ILE A 401 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.93e-01 chirality pdb=" CA VAL A 405 " pdb=" N VAL A 405 " pdb=" C VAL A 405 " pdb=" CB VAL A 405 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.84e-01 chirality pdb=" CA VAL A 292 " pdb=" N VAL A 292 " pdb=" C VAL A 292 " pdb=" CB VAL A 292 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.81e-01 ... (remaining 566 not shown) Planarity restraints: 613 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 419 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO A 420 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 420 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 420 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 418 " -0.021 5.00e-02 4.00e+02 3.26e-02 1.70e+00 pdb=" N PRO A 419 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 419 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 419 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 358 " 0.016 5.00e-02 4.00e+02 2.43e-02 9.41e-01 pdb=" N PRO A 359 " -0.042 5.00e-02 4.00e+02 pdb=" CA PRO A 359 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 359 " 0.013 5.00e-02 4.00e+02 ... (remaining 610 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 924 2.81 - 3.33: 3215 3.33 - 3.85: 5926 3.85 - 4.38: 6908 4.38 - 4.90: 11870 Nonbonded interactions: 28843 Sorted by model distance: nonbonded pdb=" OD2 ASP A 74 " pdb=" OG SER A 76 " model vdw 2.286 3.040 nonbonded pdb=" O ALA A 231 " pdb=" OG1 THR A 234 " model vdw 2.388 3.040 nonbonded pdb=" O VAL A 277 " pdb=" OG SER A 329 " model vdw 2.390 3.040 nonbonded pdb=" OH TYR A 29 " pdb=" NE1 TRP A 58 " model vdw 2.391 3.120 nonbonded pdb=" OE2 GLU A 68 " pdb=" N ARG A 96 " model vdw 2.413 3.120 ... (remaining 28838 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: 0.00 ========== 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=0.00 max=1.00 mean=0.70 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: 13.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.650 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:6.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5551 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 : 0.002 0.023 3673 Z= 0.109 Angle : 0.507 7.329 5008 Z= 0.273 Chirality : 0.044 0.125 569 Planarity : 0.004 0.041 613 Dihedral : 10.482 68.887 1404 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.27 % Allowed : 2.14 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.69 (0.37), residues: 440 helix: -0.07 (0.48), residues: 93 sheet: -0.11 (0.60), residues: 83 loop : -0.67 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 134 TYR 0.012 0.002 TYR A 167 PHE 0.005 0.001 PHE A 123 TRP 0.004 0.001 TRP A 78 HIS 0.005 0.001 HIS A 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.11 ( 3673) covalent geometry : angle 0.50747 / 0.27 ( 5008) hydrogen bonds : bond 0.21255 / 15.44 ( 128) hydrogen bonds : angle 8.23571 / 5.98 ( 370) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 69 time to evaluate : 0.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 THR cc_start: 0.6986 (p) cc_final: 0.5496 (t) REVERT: A 243 ASP cc_start: 0.5976 (m-30) cc_final: 0.5723 (t0) REVERT: A 254 TYR cc_start: 0.4476 (m-80) cc_final: 0.4154 (m-80) outliers start: 1 outliers final: 0 residues processed: 70 average time/residue: 0.5446 time to fit residues: 39.1231 Evaluate side-chains 34 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 20.0000 chunk 26 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 30.0000 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 30.0000 chunk 25 optimal weight: 20.0000 chunk 19 optimal weight: 30.0000 chunk 30 optimal weight: 6.9990 chunk 22 optimal weight: 50.0000 chunk 37 optimal weight: 40.0000 overall best weight: 9.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 349 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.104746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.086750 restraints weight = 14466.142| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 2.65 r_work: 0.3767 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3705 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3680 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3680 r_free = 0.3680 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1041 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3671 r_free = 0.3671 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1056 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (13 function evaluations) r_final: 0.3671 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3673 Z= 0.184 Angle : 0.723 13.390 5008 Z= 0.367 Chirality : 0.049 0.153 569 Planarity : 0.005 0.042 613 Dihedral : 7.832 58.313 564 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.14 % Allowed : 13.14 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.36 (0.39), residues: 440 helix: 0.43 (0.52), residues: 96 sheet: -0.05 (0.50), residues: 110 loop : -0.55 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 37 TYR 0.017 0.002 TYR A 183 PHE 0.009 0.001 PHE A 310 TRP 0.006 0.002 TRP A 78 HIS 0.009 0.002 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.18 ( 3673) covalent geometry : angle 0.72256 / 0.37 ( 5008) hydrogen bonds : bond 0.04709 / 3.23 ( 128) hydrogen bonds : angle 5.99224 / 4.12 ( 370) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.085 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: -0.2458 (mmt) cc_final: -0.2792 (mmm) REVERT: A 155 MET cc_start: 0.7507 (mtp) cc_final: 0.7273 (pmt) REVERT: A 276 MET cc_start: 0.5914 (mtp) cc_final: 0.5235 (ttm) outliers start: 8 outliers final: 2 residues processed: 37 average time/residue: 0.5857 time to fit residues: 22.3131 Evaluate side-chains 23 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 330 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 22 optimal weight: 50.0000 chunk 13 optimal weight: 50.0000 chunk 41 optimal weight: 5.9990 chunk 2 optimal weight: 50.0000 chunk 12 optimal weight: 40.0000 chunk 28 optimal weight: 40.0000 chunk 33 optimal weight: 0.6980 chunk 43 optimal weight: 20.0000 chunk 0 optimal weight: 50.0000 chunk 9 optimal weight: 40.0000 chunk 15 optimal weight: 6.9990 overall best weight: 14.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 GLN A 314 ASN A 339 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.101117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.084807 restraints weight = 14015.487| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 4.89 r_work: 0.3668 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3635 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3635 r_free = 0.3635 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1056 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3635 r_free = 0.3635 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1057 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3635 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.4497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 3673 Z= 0.250 Angle : 0.790 14.670 5008 Z= 0.403 Chirality : 0.049 0.152 569 Planarity : 0.006 0.055 613 Dihedral : 8.402 54.195 564 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.41 % Allowed : 15.28 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.71 (0.37), residues: 440 helix: 0.43 (0.50), residues: 95 sheet: -0.17 (0.56), residues: 83 loop : -0.90 (0.35), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 266 TYR 0.015 0.003 TYR A 183 PHE 0.026 0.003 PHE A 211 TRP 0.007 0.001 TRP A 196 HIS 0.007 0.002 HIS A 349 Details of bonding type rmsd/Z covalent geometry : bond 0.00536 / 0.25 ( 3673) covalent geometry : angle 0.79011 / 0.40 ( 5008) hydrogen bonds : bond 0.05406 / 3.78 ( 128) hydrogen bonds : angle 5.68073 / 3.97 ( 370) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 24 time to evaluate : 0.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.6172 (mtp) cc_final: 0.5457 (ttm) REVERT: A 290 LYS cc_start: 0.6251 (OUTLIER) cc_final: 0.4810 (tppt) REVERT: A 310 PHE cc_start: 0.8801 (p90) cc_final: 0.7906 (p90) REVERT: A 404 MET cc_start: 0.7467 (OUTLIER) cc_final: 0.7106 (mmm) outliers start: 9 outliers final: 1 residues processed: 32 average time/residue: 0.4849 time to fit residues: 16.1143 Evaluate side-chains 24 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 404 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 3 optimal weight: 40.0000 chunk 43 optimal weight: 8.9990 chunk 6 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 36 optimal weight: 0.4980 chunk 19 optimal weight: 50.0000 chunk 0 optimal weight: 40.0000 chunk 34 optimal weight: 7.9990 overall best weight: 5.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.101593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.083543 restraints weight = 13527.688| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 2.48 r_work: 0.3740 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3681 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3655 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3655 r_free = 0.3655 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1057 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3655 r_free = 0.3655 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1057 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3655 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.4752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3673 Z= 0.128 Angle : 0.632 9.089 5008 Z= 0.319 Chirality : 0.046 0.144 569 Planarity : 0.005 0.056 613 Dihedral : 7.768 55.980 564 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.54 % Allowed : 15.82 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.57 (0.37), residues: 440 helix: 0.60 (0.51), residues: 95 sheet: -0.23 (0.54), residues: 92 loop : -0.79 (0.36), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 37 TYR 0.012 0.002 TYR A 162 PHE 0.029 0.002 PHE A 211 TRP 0.005 0.001 TRP A 196 HIS 0.005 0.001 HIS A 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 3673) covalent geometry : angle 0.63184 / 0.32 ( 5008) hydrogen bonds : bond 0.03875 / 2.79 ( 128) hydrogen bonds : angle 5.21630 / 3.62 ( 370) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.141 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: -0.2138 (mmt) cc_final: -0.2642 (mmm) REVERT: A 276 MET cc_start: 0.6113 (mtp) cc_final: 0.5499 (ttm) REVERT: A 310 PHE cc_start: 0.8687 (p90) cc_final: 0.7779 (p90) outliers start: 2 outliers final: 0 residues processed: 22 average time/residue: 0.5983 time to fit residues: 13.7119 Evaluate side-chains 19 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 2 optimal weight: 50.0000 chunk 10 optimal weight: 10.0000 chunk 28 optimal weight: 30.0000 chunk 15 optimal weight: 0.0970 chunk 30 optimal weight: 9.9990 chunk 6 optimal weight: 50.0000 chunk 42 optimal weight: 40.0000 chunk 20 optimal weight: 40.0000 chunk 43 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 overall best weight: 7.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.101150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.082957 restraints weight = 13896.627| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 2.59 r_work: 0.3721 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3658 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3634 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3634 r_free = 0.3634 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1057 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3635 r_free = 0.3635 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1057 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3635 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.5132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3673 Z= 0.144 Angle : 0.631 8.949 5008 Z= 0.319 Chirality : 0.045 0.144 569 Planarity : 0.005 0.055 613 Dihedral : 7.436 54.119 564 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.34 % Allowed : 16.09 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.25 (0.38), residues: 440 helix: 0.88 (0.51), residues: 95 sheet: 0.07 (0.52), residues: 102 loop : -0.65 (0.37), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 37 TYR 0.012 0.002 TYR A 162 PHE 0.036 0.002 PHE A 211 TRP 0.005 0.001 TRP A 196 HIS 0.004 0.001 HIS A 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 3673) covalent geometry : angle 0.63122 / 0.32 ( 5008) hydrogen bonds : bond 0.04000 / 2.80 ( 128) hydrogen bonds : angle 5.09173 / 3.57 ( 370) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 0.204 Fit side-chains revert: symmetry clash REVERT: A 113 VAL cc_start: 0.8976 (t) cc_final: 0.8437 (m) REVERT: A 165 LYS cc_start: 0.8458 (mmpt) cc_final: 0.8086 (pmtt) REVERT: A 276 MET cc_start: 0.6190 (mtp) cc_final: 0.5534 (ttm) REVERT: A 290 LYS cc_start: 0.6064 (OUTLIER) cc_final: 0.4818 (tppt) REVERT: A 310 PHE cc_start: 0.8704 (p90) cc_final: 0.7791 (p90) REVERT: A 404 MET cc_start: 0.7454 (OUTLIER) cc_final: 0.7142 (mmm) outliers start: 5 outliers final: 1 residues processed: 24 average time/residue: 0.4783 time to fit residues: 12.0915 Evaluate side-chains 22 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 404 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 18 optimal weight: 0.8980 chunk 41 optimal weight: 20.0000 chunk 29 optimal weight: 20.0000 chunk 6 optimal weight: 50.0000 chunk 28 optimal weight: 40.0000 chunk 30 optimal weight: 8.9990 chunk 3 optimal weight: 8.9990 chunk 1 optimal weight: 40.0000 chunk 8 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 11 optimal weight: 50.0000 overall best weight: 6.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.101593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.085300 restraints weight = 13708.612| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 4.69 r_work: 0.3680 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3651 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3651 r_free = 0.3651 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1057 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3651 r_free = 0.3651 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1058 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3651 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.5414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3673 Z= 0.135 Angle : 0.606 7.924 5008 Z= 0.310 Chirality : 0.045 0.142 569 Planarity : 0.005 0.056 613 Dihedral : 7.064 54.892 564 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.80 % Allowed : 16.35 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.31 (0.38), residues: 440 helix: 0.76 (0.52), residues: 95 sheet: 0.03 (0.53), residues: 100 loop : -0.66 (0.37), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 37 TYR 0.009 0.002 TYR A 357 PHE 0.029 0.002 PHE A 211 TRP 0.020 0.002 TRP A 58 HIS 0.004 0.001 HIS A 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 ( 3673) covalent geometry : angle 0.60607 / 0.31 ( 5008) hydrogen bonds : bond 0.03785 / 2.65 ( 128) hydrogen bonds : angle 5.01855 / 3.52 ( 370) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.139 Fit side-chains revert: symmetry clash REVERT: A 113 VAL cc_start: 0.8947 (t) cc_final: 0.8370 (m) REVERT: A 165 LYS cc_start: 0.8469 (mmpt) cc_final: 0.8015 (ptpp) REVERT: A 276 MET cc_start: 0.6114 (mtp) cc_final: 0.5455 (ttm) REVERT: A 290 LYS cc_start: 0.6072 (OUTLIER) cc_final: 0.4564 (tppt) REVERT: A 310 PHE cc_start: 0.8715 (p90) cc_final: 0.7915 (p90) REVERT: A 404 MET cc_start: 0.7363 (OUTLIER) cc_final: 0.6959 (mmt) outliers start: 3 outliers final: 0 residues processed: 22 average time/residue: 0.5893 time to fit residues: 13.4906 Evaluate side-chains 21 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 19 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 404 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 40 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 20 optimal weight: 40.0000 chunk 21 optimal weight: 40.0000 chunk 7 optimal weight: 30.0000 chunk 31 optimal weight: 30.0000 chunk 8 optimal weight: 30.0000 chunk 9 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 38 optimal weight: 20.0000 chunk 19 optimal weight: 8.9990 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 200 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.100874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.084742 restraints weight = 14043.304| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 4.78 r_work: 0.3671 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3638 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3638 r_free = 0.3638 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1058 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3638 r_free = 0.3638 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1058 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3638 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.5771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3673 Z= 0.156 Angle : 0.618 8.552 5008 Z= 0.317 Chirality : 0.045 0.139 569 Planarity : 0.005 0.057 613 Dihedral : 7.070 53.140 564 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.88 % Allowed : 16.09 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.29 (0.39), residues: 440 helix: 0.89 (0.53), residues: 95 sheet: -0.05 (0.51), residues: 108 loop : -0.67 (0.39), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 37 TYR 0.011 0.001 TYR A 162 PHE 0.011 0.002 PHE A 340 TRP 0.008 0.001 TRP A 58 HIS 0.005 0.001 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 ( 3673) covalent geometry : angle 0.61835 / 0.32 ( 5008) hydrogen bonds : bond 0.03927 / 2.71 ( 128) hydrogen bonds : angle 5.04271 / 3.54 ( 370) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 20 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.7819 (pptt) REVERT: A 165 LYS cc_start: 0.8431 (mmpt) cc_final: 0.7996 (ptpp) REVERT: A 276 MET cc_start: 0.6094 (mtp) cc_final: 0.5423 (ttm) REVERT: A 290 LYS cc_start: 0.6296 (OUTLIER) cc_final: 0.4753 (tppt) REVERT: A 310 PHE cc_start: 0.8710 (p90) cc_final: 0.7921 (p90) REVERT: A 404 MET cc_start: 0.7300 (OUTLIER) cc_final: 0.6955 (mmt) outliers start: 7 outliers final: 1 residues processed: 25 average time/residue: 0.6195 time to fit residues: 16.1139 Evaluate side-chains 24 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 404 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 4.9990 chunk 0 optimal weight: 60.0000 chunk 39 optimal weight: 6.9990 chunk 5 optimal weight: 30.0000 chunk 37 optimal weight: 30.0000 chunk 10 optimal weight: 20.0000 chunk 26 optimal weight: 7.9990 chunk 27 optimal weight: 0.0470 chunk 11 optimal weight: 50.0000 chunk 28 optimal weight: 8.9990 chunk 13 optimal weight: 8.9990 overall best weight: 5.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 200 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.100977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.082892 restraints weight = 13839.377| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 2.54 r_work: 0.3724 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3661 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3637 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3637 r_free = 0.3637 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1058 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3637 r_free = 0.3637 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1057 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3637 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.5976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3673 Z= 0.121 Angle : 0.602 8.739 5008 Z= 0.302 Chirality : 0.045 0.140 569 Planarity : 0.005 0.056 613 Dihedral : 6.800 55.991 564 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.34 % Allowed : 16.35 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.33 (0.39), residues: 440 helix: 0.85 (0.53), residues: 97 sheet: -0.01 (0.52), residues: 108 loop : -0.74 (0.38), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 37 TYR 0.010 0.001 TYR A 357 PHE 0.012 0.001 PHE A 340 TRP 0.010 0.001 TRP A 58 HIS 0.007 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 3673) covalent geometry : angle 0.60156 / 0.30 ( 5008) hydrogen bonds : bond 0.03445 / 2.42 ( 128) hydrogen bonds : angle 4.93012 / 3.44 ( 370) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 0.092 Fit side-chains revert: symmetry clash REVERT: A 26 HIS cc_start: 0.8220 (t70) cc_final: 0.7731 (t-90) REVERT: A 113 VAL cc_start: 0.8816 (t) cc_final: 0.8190 (m) REVERT: A 165 LYS cc_start: 0.8500 (mmpt) cc_final: 0.8177 (pmtt) REVERT: A 276 MET cc_start: 0.6127 (mtp) cc_final: 0.5451 (ttm) REVERT: A 290 LYS cc_start: 0.6057 (OUTLIER) cc_final: 0.4388 (tppt) REVERT: A 310 PHE cc_start: 0.8715 (p90) cc_final: 0.7973 (p90) REVERT: A 404 MET cc_start: 0.7270 (OUTLIER) cc_final: 0.6942 (mmt) outliers start: 5 outliers final: 1 residues processed: 24 average time/residue: 0.5269 time to fit residues: 13.1655 Evaluate side-chains 23 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 404 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 11 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 2 optimal weight: 50.0000 chunk 10 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 43 optimal weight: 10.0000 chunk 16 optimal weight: 30.0000 chunk 25 optimal weight: 20.0000 chunk 6 optimal weight: 50.0000 chunk 23 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 200 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.100641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.082470 restraints weight = 13879.407| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 2.50 r_work: 0.3713 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3651 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3628 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3628 r_free = 0.3628 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1057 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3628 r_free = 0.3628 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1057 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3628 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.6147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3673 Z= 0.144 Angle : 0.616 9.013 5008 Z= 0.309 Chirality : 0.045 0.136 569 Planarity : 0.005 0.059 613 Dihedral : 6.935 53.404 564 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.80 % Allowed : 18.23 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.20 (0.39), residues: 440 helix: 0.95 (0.53), residues: 97 sheet: 0.23 (0.50), residues: 115 loop : -0.77 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 67 TYR 0.010 0.001 TYR A 162 PHE 0.012 0.002 PHE A 211 TRP 0.007 0.001 TRP A 58 HIS 0.005 0.001 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 ( 3673) covalent geometry : angle 0.61620 / 0.31 ( 5008) hydrogen bonds : bond 0.03659 / 2.55 ( 128) hydrogen bonds : angle 4.94725 / 3.46 ( 370) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 18 time to evaluate : 0.144 Fit side-chains revert: symmetry clash REVERT: A 165 LYS cc_start: 0.8493 (mmpt) cc_final: 0.8170 (pmtt) REVERT: A 276 MET cc_start: 0.6186 (mtp) cc_final: 0.5521 (ttm) REVERT: A 290 LYS cc_start: 0.6119 (OUTLIER) cc_final: 0.4381 (tppt) REVERT: A 310 PHE cc_start: 0.8706 (p90) cc_final: 0.7967 (p90) REVERT: A 404 MET cc_start: 0.7298 (OUTLIER) cc_final: 0.6914 (mmp) outliers start: 3 outliers final: 2 residues processed: 20 average time/residue: 0.6587 time to fit residues: 13.6812 Evaluate side-chains 22 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 18 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 404 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 17 optimal weight: 30.0000 chunk 39 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 30 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 35 optimal weight: 30.0000 chunk 10 optimal weight: 10.0000 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 200 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.100786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.082762 restraints weight = 13882.750| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 2.55 r_work: 0.3722 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3659 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3635 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3635 r_free = 0.3635 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1057 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3635 r_free = 0.3635 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1057 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3635 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.6326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3673 Z= 0.121 Angle : 0.610 12.279 5008 Z= 0.300 Chirality : 0.045 0.137 569 Planarity : 0.005 0.056 613 Dihedral : 6.782 55.788 564 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.07 % Allowed : 17.69 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.23 (0.39), residues: 440 helix: 1.02 (0.53), residues: 97 sheet: -0.00 (0.53), residues: 106 loop : -0.69 (0.37), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 37 TYR 0.009 0.001 TYR A 357 PHE 0.012 0.001 PHE A 340 TRP 0.011 0.001 TRP A 210 HIS 0.005 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 3673) covalent geometry : angle 0.61041 / 0.30 ( 5008) hydrogen bonds : bond 0.03328 / 2.34 ( 128) hydrogen bonds : angle 4.95886 / 3.46 ( 370) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 18 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: A 165 LYS cc_start: 0.8458 (mmpt) cc_final: 0.8167 (pmtt) REVERT: A 208 MET cc_start: 0.7105 (tmm) cc_final: 0.6788 (tpp) REVERT: A 276 MET cc_start: 0.6108 (mtp) cc_final: 0.5428 (ttm) REVERT: A 290 LYS cc_start: 0.6065 (OUTLIER) cc_final: 0.4115 (tppt) REVERT: A 310 PHE cc_start: 0.8724 (p90) cc_final: 0.7993 (p90) REVERT: A 404 MET cc_start: 0.7242 (OUTLIER) cc_final: 0.6900 (mmt) outliers start: 4 outliers final: 1 residues processed: 20 average time/residue: 0.6516 time to fit residues: 13.5541 Evaluate side-chains 21 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 18 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 404 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 29 optimal weight: 6.9990 chunk 34 optimal weight: 30.0000 chunk 8 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 40.0000 chunk 3 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 16 optimal weight: 30.0000 chunk 14 optimal weight: 10.0000 chunk 35 optimal weight: 30.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.100839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.082758 restraints weight = 13663.301| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 2.53 r_work: 0.3719 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3661 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3637 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3637 r_free = 0.3637 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1057 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3637 r_free = 0.3637 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1057 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3637 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.6447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3673 Z= 0.128 Angle : 0.609 10.878 5008 Z= 0.302 Chirality : 0.045 0.137 569 Planarity : 0.005 0.057 613 Dihedral : 6.777 54.262 564 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.07 % Allowed : 17.43 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.11 (0.39), residues: 440 helix: 1.05 (0.53), residues: 97 sheet: 0.19 (0.51), residues: 113 loop : -0.66 (0.39), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 423 TYR 0.010 0.001 TYR A 162 PHE 0.013 0.002 PHE A 211 TRP 0.008 0.001 TRP A 58 HIS 0.004 0.001 HIS A 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 ( 3673) covalent geometry : angle 0.60872 / 0.30 ( 5008) hydrogen bonds : bond 0.03453 / 2.39 ( 128) hydrogen bonds : angle 4.93860 / 3.44 ( 370) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1794.12 seconds wall clock time: 31 minutes 17.71 seconds (1877.71 seconds total)