Starting phenix.real_space_refine on Sun Apr 27 00:10:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b1k_44082/04_2025/9b1k_44082.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b1k_44082/04_2025/9b1k_44082.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b1k_44082/04_2025/9b1k_44082.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b1k_44082/04_2025/9b1k_44082.map" model { file = "/net/cci-nas-00/data/ceres_data/9b1k_44082/04_2025/9b1k_44082.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b1k_44082/04_2025/9b1k_44082.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 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: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 2548 2.51 5 N 661 2.21 5 O 672 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-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 3911 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3899 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 29, 'TRANS': 482} Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'URC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.28, per 1000 atoms: 0.84 Number of scatterers: 3911 At special positions: 0 Unit cell: (57.761, 102.542, 89.562, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 672 8.00 N 661 7.00 C 2548 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 113 " distance=2.03 Simple disulfide: pdb=" SG CYS A 85 " - pdb=" SG CYS A 136 " distance=2.03 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: 0.91 Conformation dependent library (CDL) restraints added in 437.0 milliseconds 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 944 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 2 sheets defined 82.8% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 3 through 11 removed outlier: 3.512A pdb=" N LEU A 9 " --> pdb=" O GLU A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 37 Processing helix chain 'A' and resid 37 through 42 Processing helix chain 'A' and resid 51 through 56 Processing helix chain 'A' and resid 65 through 74 removed outlier: 3.515A pdb=" N ALA A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 97 removed outlier: 3.786A pdb=" N ASP A 97 " --> pdb=" O GLN A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 108 No H-bonds generated for 'chain 'A' and resid 106 through 108' Processing helix chain 'A' and resid 127 through 133 Processing helix chain 'A' and resid 135 through 139 Processing helix chain 'A' and resid 140 through 168 removed outlier: 3.965A pdb=" N GLY A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) Proline residue: A 162 - end of helix Processing helix chain 'A' and resid 168 through 189 removed outlier: 3.622A pdb=" N TRP A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE A 189 " --> pdb=" O THR A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 220 removed outlier: 3.717A pdb=" N ALA A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY A 209 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY A 215 " --> pdb=" O MET A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 222 No H-bonds generated for 'chain 'A' and resid 221 through 222' Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'A' and resid 226 through 252 removed outlier: 4.297A pdb=" N PHE A 238 " --> pdb=" O ASN A 234 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER A 239 " --> pdb=" O SER A 235 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY A 243 " --> pdb=" O SER A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 262 removed outlier: 3.828A pdb=" N LEU A 260 " --> pdb=" O THR A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 276 removed outlier: 4.080A pdb=" N LEU A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU A 271 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 286 Processing helix chain 'A' and resid 288 through 304 removed outlier: 4.163A pdb=" N GLN A 294 " --> pdb=" O ASP A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.911A pdb=" N ALA A 308 " --> pdb=" O HIS A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 320 removed outlier: 3.536A pdb=" N VAL A 320 " --> pdb=" O LEU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 327 Processing helix chain 'A' and resid 334 through 339 removed outlier: 3.518A pdb=" N VAL A 339 " --> pdb=" O ASP A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 364 removed outlier: 3.561A pdb=" N PHE A 344 " --> pdb=" O PRO A 340 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 363 " --> pdb=" O THR A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 370 Processing helix chain 'A' and resid 373 through 399 removed outlier: 3.572A pdb=" N ILE A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY A 382 " --> pdb=" O GLN A 378 " (cutoff:3.500A) Proline residue: A 387 - end of helix Processing helix chain 'A' and resid 400 through 418 removed outlier: 3.613A pdb=" N THR A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA A 406 " --> pdb=" O ARG A 402 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA A 407 " --> pdb=" O PRO A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 421 No H-bonds generated for 'chain 'A' and resid 419 through 421' Processing helix chain 'A' and resid 426 through 455 Processing helix chain 'A' and resid 460 through 485 Proline residue: A 480 - end of helix Processing helix chain 'A' and resid 486 through 489 Processing helix chain 'A' and resid 490 through 509 removed outlier: 3.933A pdb=" N VAL A 500 " --> pdb=" O VAL A 496 " (cutoff:3.500A) Proline residue: A 501 - end of helix removed outlier: 3.758A pdb=" N LEU A 509 " --> pdb=" O GLY A 505 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 87 through 88 269 hydrogen bonds defined for protein. 777 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.01 Time building geometry restraints manager: 1.08 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: 1232 1.34 - 1.46: 955 1.46 - 1.58: 1777 1.58 - 1.70: 0 1.70 - 1.82: 47 Bond restraints: 4011 Sorted by residual: bond pdb=" C2 URC A 901 " pdb=" O11 URC A 901 " ideal model delta sigma weight residual 1.213 1.360 -0.147 2.00e-02 2.50e+03 5.39e+01 bond pdb=" C8 URC A 901 " pdb=" O24 URC A 901 " ideal model delta sigma weight residual 1.215 1.350 -0.135 2.00e-02 2.50e+03 4.58e+01 bond pdb=" C4 URC A 901 " pdb=" C5 URC A 901 " ideal model delta sigma weight residual 1.358 1.488 -0.130 2.00e-02 2.50e+03 4.21e+01 bond pdb=" C6 URC A 901 " pdb=" O13 URC A 901 " ideal model delta sigma weight residual 1.218 1.345 -0.127 2.00e-02 2.50e+03 4.05e+01 bond pdb=" C4 URC A 901 " pdb=" N9 URC A 901 " ideal model delta sigma weight residual 1.352 1.425 -0.073 2.00e-02 2.50e+03 1.34e+01 ... (remaining 4006 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 5417 2.68 - 5.35: 44 5.35 - 8.03: 5 8.03 - 10.70: 4 10.70 - 13.38: 3 Bond angle restraints: 5473 Sorted by residual: angle pdb=" N1 URC A 901 " pdb=" C2 URC A 901 " pdb=" N3 URC A 901 " ideal model delta sigma weight residual 114.62 128.00 -13.38 3.00e+00 1.11e-01 1.99e+01 angle pdb=" C2 URC A 901 " pdb=" N1 URC A 901 " pdb=" C6 URC A 901 " ideal model delta sigma weight residual 129.31 117.61 11.70 3.00e+00 1.11e-01 1.52e+01 angle pdb=" N7 URC A 901 " pdb=" C8 URC A 901 " pdb=" N9 URC A 901 " ideal model delta sigma weight residual 104.73 116.27 -11.54 3.00e+00 1.11e-01 1.48e+01 angle pdb=" C5 URC A 901 " pdb=" C6 URC A 901 " pdb=" N1 URC A 901 " ideal model delta sigma weight residual 111.19 121.73 -10.54 3.00e+00 1.11e-01 1.23e+01 angle pdb=" N7 URC A 901 " pdb=" C8 URC A 901 " pdb=" O24 URC A 901 " ideal model delta sigma weight residual 129.09 119.74 9.35 3.00e+00 1.11e-01 9.72e+00 ... (remaining 5468 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.54: 2189 15.54 - 31.08: 143 31.08 - 46.62: 16 46.62 - 62.16: 5 62.16 - 77.70: 2 Dihedral angle restraints: 2355 sinusoidal: 892 harmonic: 1463 Sorted by residual: dihedral pdb=" CA GLU A 329 " pdb=" C GLU A 329 " pdb=" N PRO A 330 " pdb=" CA PRO A 330 " ideal model delta harmonic sigma weight residual 180.00 162.35 17.65 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA LYS A 286 " pdb=" C LYS A 286 " pdb=" N GLY A 287 " pdb=" CA GLY A 287 " ideal model delta harmonic sigma weight residual 180.00 162.38 17.62 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CB MET A 36 " pdb=" CG MET A 36 " pdb=" SD MET A 36 " pdb=" CE MET A 36 " ideal model delta sinusoidal sigma weight residual 180.00 129.26 50.74 3 1.50e+01 4.44e-03 8.94e+00 ... (remaining 2352 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 380 0.026 - 0.053: 177 0.053 - 0.079: 52 0.079 - 0.105: 25 0.105 - 0.131: 8 Chirality restraints: 642 Sorted by residual: chirality pdb=" CA PRO A 501 " pdb=" N PRO A 501 " pdb=" C PRO A 501 " pdb=" CB PRO A 501 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.32e-01 chirality pdb=" CA VAL A 422 " pdb=" N VAL A 422 " pdb=" C VAL A 422 " pdb=" CB VAL A 422 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.05e-01 chirality pdb=" CA VAL A 118 " pdb=" N VAL A 118 " pdb=" C VAL A 118 " pdb=" CB VAL A 118 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.11 2.00e-01 2.50e+01 3.30e-01 ... (remaining 639 not shown) Planarity restraints: 680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 276 " -0.022 5.00e-02 4.00e+02 3.36e-02 1.81e+00 pdb=" N PRO A 277 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 277 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 277 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 264 " 0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO A 265 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 265 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 265 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 479 " 0.018 5.00e-02 4.00e+02 2.72e-02 1.18e+00 pdb=" N PRO A 480 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 480 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 480 " 0.015 5.00e-02 4.00e+02 ... (remaining 677 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 968 2.79 - 3.32: 3936 3.32 - 3.85: 6497 3.85 - 4.37: 7738 4.37 - 4.90: 12839 Nonbonded interactions: 31978 Sorted by model distance: nonbonded pdb=" OE1 GLU A 220 " pdb=" OG SER A 279 " model vdw 2.265 3.040 nonbonded pdb=" O TRP A 30 " pdb=" OG1 THR A 33 " model vdw 2.346 3.040 nonbonded pdb=" OG SER A 239 " pdb=" OD2 ASP A 385 " model vdw 2.410 3.040 nonbonded pdb=" O PHE A 270 " pdb=" OG SER A 273 " model vdw 2.411 3.040 nonbonded pdb=" OH TYR A 451 " pdb=" O PRO A 512 " model vdw 2.424 3.040 ... (remaining 31973 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 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: 2.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.430 Find NCS groups from input model: 0.030 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: 0.010 Load rotamer database and sin/cos tables:3.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 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 : 0.006 0.147 4013 Z= 0.298 Angle : 0.741 13.375 5477 Z= 0.355 Chirality : 0.037 0.131 642 Planarity : 0.004 0.034 680 Dihedral : 10.547 77.700 1405 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 1.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.37), residues: 510 helix: 0.05 (0.26), residues: 375 sheet: -1.86 (1.54), residues: 10 loop : 0.91 (0.61), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 491 HIS 0.002 0.000 HIS A 83 PHE 0.014 0.001 PHE A 270 TYR 0.011 0.001 TYR A 272 ARG 0.004 0.001 ARG A 15 Details of bonding type rmsd hydrogen bonds : bond 0.13338 ( 269) hydrogen bonds : angle 5.87484 ( 777) SS BOND : bond 0.00042 ( 2) SS BOND : angle 2.07348 ( 4) covalent geometry : bond 0.00606 ( 4011) covalent geometry : angle 0.73883 ( 5473) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: A 22 MET cc_start: 0.7160 (ttm) cc_final: 0.6490 (ttp) REVERT: A 56 ASN cc_start: 0.7463 (t0) cc_final: 0.7147 (t0) REVERT: A 166 ARG cc_start: 0.7691 (ttt180) cc_final: 0.7178 (tpp80) REVERT: A 231 MET cc_start: 0.7036 (mmm) cc_final: 0.6787 (mmt) REVERT: A 234 ASN cc_start: 0.8722 (t0) cc_final: 0.8462 (t0) REVERT: A 291 GLN cc_start: 0.7796 (mt0) cc_final: 0.7228 (tt0) REVERT: A 367 LEU cc_start: 0.8448 (mt) cc_final: 0.8182 (mp) REVERT: A 374 ILE cc_start: 0.7877 (pt) cc_final: 0.7643 (tt) REVERT: A 491 TRP cc_start: 0.4952 (t60) cc_final: 0.4749 (t60) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1531 time to fit residues: 15.8615 Evaluate side-chains 59 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 43 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 0.2980 chunk 20 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.190910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.148156 restraints weight = 4578.043| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.28 r_work: 0.3400 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4013 Z= 0.145 Angle : 0.574 5.662 5477 Z= 0.294 Chirality : 0.039 0.133 642 Planarity : 0.005 0.047 680 Dihedral : 4.411 16.247 545 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.69 % Allowed : 6.54 % Favored : 91.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.38), residues: 510 helix: 0.72 (0.27), residues: 379 sheet: None (None), residues: 0 loop : 0.79 (0.56), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 50 HIS 0.002 0.001 HIS A 424 PHE 0.010 0.001 PHE A 358 TYR 0.017 0.002 TYR A 272 ARG 0.011 0.001 ARG A 297 Details of bonding type rmsd hydrogen bonds : bond 0.05090 ( 269) hydrogen bonds : angle 4.66476 ( 777) SS BOND : bond 0.00086 ( 2) SS BOND : angle 2.08856 ( 4) covalent geometry : bond 0.00328 ( 4011) covalent geometry : angle 0.57128 ( 5473) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.381 Fit side-chains REVERT: A 22 MET cc_start: 0.6872 (ttm) cc_final: 0.6191 (ttp) REVERT: A 56 ASN cc_start: 0.7209 (t0) cc_final: 0.6785 (t0) REVERT: A 166 ARG cc_start: 0.7631 (ttt180) cc_final: 0.6919 (tpp-160) REVERT: A 231 MET cc_start: 0.6995 (mmm) cc_final: 0.6748 (mmt) REVERT: A 320 VAL cc_start: 0.3598 (OUTLIER) cc_final: 0.3395 (p) outliers start: 7 outliers final: 3 residues processed: 66 average time/residue: 0.1399 time to fit residues: 12.1659 Evaluate side-chains 57 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 399 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 46 optimal weight: 5.9990 chunk 18 optimal weight: 0.0030 chunk 39 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.191982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.149392 restraints weight = 4565.978| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.30 r_work: 0.3411 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4013 Z= 0.131 Angle : 0.546 6.278 5477 Z= 0.274 Chirality : 0.038 0.129 642 Planarity : 0.005 0.040 680 Dihedral : 4.166 15.375 545 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.94 % Allowed : 8.23 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.38), residues: 510 helix: 0.94 (0.27), residues: 380 sheet: -2.49 (1.64), residues: 10 loop : 0.69 (0.58), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 491 HIS 0.002 0.000 HIS A 139 PHE 0.009 0.001 PHE A 358 TYR 0.018 0.001 TYR A 272 ARG 0.004 0.000 ARG A 15 Details of bonding type rmsd hydrogen bonds : bond 0.04709 ( 269) hydrogen bonds : angle 4.43878 ( 777) SS BOND : bond 0.00098 ( 2) SS BOND : angle 1.84663 ( 4) covalent geometry : bond 0.00296 ( 4011) covalent geometry : angle 0.54380 ( 5473) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.350 Fit side-chains REVERT: A 5 GLU cc_start: 0.6761 (pm20) cc_final: 0.6431 (pm20) REVERT: A 22 MET cc_start: 0.6758 (ttm) cc_final: 0.6548 (mtt) REVERT: A 56 ASN cc_start: 0.7154 (t0) cc_final: 0.6707 (t0) REVERT: A 166 ARG cc_start: 0.7657 (ttt180) cc_final: 0.7022 (tpp80) REVERT: A 491 TRP cc_start: 0.4863 (t60) cc_final: 0.4521 (p-90) outliers start: 8 outliers final: 4 residues processed: 65 average time/residue: 0.1247 time to fit residues: 10.7866 Evaluate side-chains 60 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 374 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 42 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.185332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.141370 restraints weight = 4607.525| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.32 r_work: 0.3395 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4013 Z= 0.146 Angle : 0.547 5.722 5477 Z= 0.274 Chirality : 0.039 0.156 642 Planarity : 0.005 0.042 680 Dihedral : 4.103 14.792 545 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.39 % Allowed : 7.26 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.37), residues: 510 helix: 0.95 (0.26), residues: 381 sheet: -2.52 (1.69), residues: 10 loop : 0.71 (0.60), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 491 HIS 0.002 0.001 HIS A 139 PHE 0.011 0.001 PHE A 358 TYR 0.020 0.002 TYR A 272 ARG 0.002 0.000 ARG A 121 Details of bonding type rmsd hydrogen bonds : bond 0.04760 ( 269) hydrogen bonds : angle 4.38864 ( 777) SS BOND : bond 0.00134 ( 2) SS BOND : angle 1.94820 ( 4) covalent geometry : bond 0.00344 ( 4011) covalent geometry : angle 0.54453 ( 5473) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.433 Fit side-chains REVERT: A 5 GLU cc_start: 0.6656 (pm20) cc_final: 0.6443 (pm20) REVERT: A 22 MET cc_start: 0.6754 (ttm) cc_final: 0.6088 (ttp) REVERT: A 56 ASN cc_start: 0.7176 (t0) cc_final: 0.6700 (t0) REVERT: A 166 ARG cc_start: 0.7615 (ttt180) cc_final: 0.6813 (tpp-160) REVERT: A 234 ASN cc_start: 0.8619 (t0) cc_final: 0.8249 (t0) REVERT: A 290 ASP cc_start: 0.7139 (t0) cc_final: 0.6938 (t0) REVERT: A 385 ASP cc_start: 0.7985 (OUTLIER) cc_final: 0.7611 (m-30) REVERT: A 491 TRP cc_start: 0.4935 (t60) cc_final: 0.4575 (p-90) outliers start: 14 outliers final: 10 residues processed: 70 average time/residue: 0.1274 time to fit residues: 11.8317 Evaluate side-chains 68 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 470 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 20 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.189610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.145751 restraints weight = 4716.363| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.37 r_work: 0.3374 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4013 Z= 0.135 Angle : 0.531 6.891 5477 Z= 0.265 Chirality : 0.038 0.137 642 Planarity : 0.005 0.043 680 Dihedral : 4.024 14.073 545 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.39 % Allowed : 8.23 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.38), residues: 510 helix: 1.03 (0.26), residues: 387 sheet: -2.42 (1.79), residues: 10 loop : 0.93 (0.63), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 50 HIS 0.001 0.000 HIS A 139 PHE 0.010 0.001 PHE A 358 TYR 0.019 0.001 TYR A 272 ARG 0.002 0.000 ARG A 121 Details of bonding type rmsd hydrogen bonds : bond 0.04538 ( 269) hydrogen bonds : angle 4.31168 ( 777) SS BOND : bond 0.00173 ( 2) SS BOND : angle 1.72041 ( 4) covalent geometry : bond 0.00311 ( 4011) covalent geometry : angle 0.52872 ( 5473) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.410 Fit side-chains REVERT: A 22 MET cc_start: 0.6793 (ttm) cc_final: 0.6506 (mtt) REVERT: A 56 ASN cc_start: 0.7220 (t0) cc_final: 0.6738 (t0) REVERT: A 166 ARG cc_start: 0.7626 (ttt180) cc_final: 0.6972 (tpp80) REVERT: A 234 ASN cc_start: 0.8598 (t0) cc_final: 0.8263 (t0) REVERT: A 293 LEU cc_start: 0.6297 (tt) cc_final: 0.6027 (tt) REVERT: A 462 MET cc_start: 0.6347 (tpt) cc_final: 0.6050 (tpt) REVERT: A 491 TRP cc_start: 0.4928 (t60) cc_final: 0.4649 (p-90) outliers start: 14 outliers final: 12 residues processed: 71 average time/residue: 0.1210 time to fit residues: 11.5266 Evaluate side-chains 67 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 470 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 9 optimal weight: 0.4980 chunk 43 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.186770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.142088 restraints weight = 4679.584| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.38 r_work: 0.3378 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4013 Z= 0.132 Angle : 0.533 6.810 5477 Z= 0.264 Chirality : 0.038 0.128 642 Planarity : 0.004 0.043 680 Dihedral : 3.960 14.041 545 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.15 % Allowed : 8.72 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.38), residues: 510 helix: 1.10 (0.26), residues: 387 sheet: -2.59 (1.81), residues: 10 loop : 0.96 (0.63), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 50 HIS 0.001 0.000 HIS A 139 PHE 0.009 0.001 PHE A 358 TYR 0.019 0.001 TYR A 272 ARG 0.002 0.000 ARG A 227 Details of bonding type rmsd hydrogen bonds : bond 0.04484 ( 269) hydrogen bonds : angle 4.31688 ( 777) SS BOND : bond 0.00191 ( 2) SS BOND : angle 1.60484 ( 4) covalent geometry : bond 0.00304 ( 4011) covalent geometry : angle 0.53116 ( 5473) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.379 Fit side-chains REVERT: A 22 MET cc_start: 0.6838 (ttm) cc_final: 0.6549 (mtt) REVERT: A 56 ASN cc_start: 0.7275 (t0) cc_final: 0.6787 (t0) REVERT: A 166 ARG cc_start: 0.7670 (ttt180) cc_final: 0.7013 (tpp80) REVERT: A 293 LEU cc_start: 0.6331 (tt) cc_final: 0.6083 (tt) REVERT: A 385 ASP cc_start: 0.7994 (OUTLIER) cc_final: 0.7628 (m-30) REVERT: A 462 MET cc_start: 0.6418 (tpt) cc_final: 0.6158 (tpt) outliers start: 13 outliers final: 11 residues processed: 64 average time/residue: 0.1258 time to fit residues: 10.8229 Evaluate side-chains 67 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 451 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 21 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 0.0870 chunk 45 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 13 optimal weight: 0.1980 chunk 20 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.193649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.151115 restraints weight = 4626.282| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.34 r_work: 0.3438 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4013 Z= 0.117 Angle : 0.502 6.693 5477 Z= 0.249 Chirality : 0.037 0.126 642 Planarity : 0.004 0.043 680 Dihedral : 3.844 13.668 545 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.91 % Allowed : 9.44 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.38), residues: 510 helix: 1.21 (0.26), residues: 388 sheet: -2.22 (1.94), residues: 10 loop : 0.97 (0.63), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 491 HIS 0.001 0.000 HIS A 139 PHE 0.011 0.001 PHE A 201 TYR 0.017 0.001 TYR A 272 ARG 0.001 0.000 ARG A 86 Details of bonding type rmsd hydrogen bonds : bond 0.04276 ( 269) hydrogen bonds : angle 4.20658 ( 777) SS BOND : bond 0.00190 ( 2) SS BOND : angle 1.37963 ( 4) covalent geometry : bond 0.00257 ( 4011) covalent geometry : angle 0.50035 ( 5473) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.427 Fit side-chains REVERT: A 22 MET cc_start: 0.6691 (ttm) cc_final: 0.6323 (ptt) REVERT: A 56 ASN cc_start: 0.7160 (t0) cc_final: 0.6650 (t0) REVERT: A 166 ARG cc_start: 0.7610 (ttt180) cc_final: 0.6915 (tpp80) REVERT: A 234 ASN cc_start: 0.8541 (t0) cc_final: 0.8318 (t0) REVERT: A 293 LEU cc_start: 0.6226 (tt) cc_final: 0.5987 (tt) REVERT: A 385 ASP cc_start: 0.7944 (OUTLIER) cc_final: 0.7515 (m-30) REVERT: A 462 MET cc_start: 0.6311 (tpt) cc_final: 0.6078 (tpt) outliers start: 12 outliers final: 10 residues processed: 70 average time/residue: 0.1350 time to fit residues: 12.7292 Evaluate side-chains 71 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 451 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 10 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 7 optimal weight: 0.0570 chunk 5 optimal weight: 0.4980 chunk 50 optimal weight: 0.0970 chunk 17 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.196272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.153745 restraints weight = 4624.201| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.33 r_work: 0.3418 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4013 Z= 0.114 Angle : 0.529 10.782 5477 Z= 0.255 Chirality : 0.037 0.125 642 Planarity : 0.004 0.043 680 Dihedral : 3.719 13.483 545 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.42 % Allowed : 10.90 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.38), residues: 510 helix: 1.46 (0.27), residues: 380 sheet: -1.93 (2.03), residues: 10 loop : 0.97 (0.60), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 50 HIS 0.001 0.000 HIS A 139 PHE 0.010 0.001 PHE A 201 TYR 0.016 0.001 TYR A 272 ARG 0.001 0.000 ARG A 86 Details of bonding type rmsd hydrogen bonds : bond 0.04144 ( 269) hydrogen bonds : angle 4.14422 ( 777) SS BOND : bond 0.00188 ( 2) SS BOND : angle 1.26803 ( 4) covalent geometry : bond 0.00249 ( 4011) covalent geometry : angle 0.52776 ( 5473) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.510 Fit side-chains REVERT: A 5 GLU cc_start: 0.7074 (pm20) cc_final: 0.6810 (pm20) REVERT: A 22 MET cc_start: 0.6755 (ttm) cc_final: 0.6466 (ptt) REVERT: A 56 ASN cc_start: 0.7202 (t0) cc_final: 0.6673 (t0) REVERT: A 166 ARG cc_start: 0.7638 (ttt180) cc_final: 0.6971 (tpp80) REVERT: A 234 ASN cc_start: 0.8512 (t0) cc_final: 0.8284 (t0) REVERT: A 293 LEU cc_start: 0.6303 (tt) cc_final: 0.6077 (tt) outliers start: 10 outliers final: 10 residues processed: 69 average time/residue: 0.2180 time to fit residues: 20.4582 Evaluate side-chains 69 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 451 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 37 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.188897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.146033 restraints weight = 4608.688| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.28 r_work: 0.3405 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4013 Z= 0.135 Angle : 0.547 8.796 5477 Z= 0.265 Chirality : 0.038 0.126 642 Planarity : 0.004 0.042 680 Dihedral : 3.777 13.323 545 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.91 % Allowed : 10.17 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.38), residues: 510 helix: 1.38 (0.26), residues: 380 sheet: -1.89 (2.08), residues: 10 loop : 1.06 (0.60), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 50 HIS 0.001 0.000 HIS A 139 PHE 0.009 0.001 PHE A 266 TYR 0.018 0.001 TYR A 272 ARG 0.002 0.000 ARG A 402 Details of bonding type rmsd hydrogen bonds : bond 0.04441 ( 269) hydrogen bonds : angle 4.22567 ( 777) SS BOND : bond 0.00207 ( 2) SS BOND : angle 1.45998 ( 4) covalent geometry : bond 0.00314 ( 4011) covalent geometry : angle 0.54588 ( 5473) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.843 Fit side-chains REVERT: A 22 MET cc_start: 0.7011 (ttm) cc_final: 0.6635 (ptt) REVERT: A 56 ASN cc_start: 0.7270 (t0) cc_final: 0.6764 (t0) REVERT: A 166 ARG cc_start: 0.7684 (ttt180) cc_final: 0.6987 (tpp80) REVERT: A 234 ASN cc_start: 0.8591 (t0) cc_final: 0.8379 (t0) REVERT: A 293 LEU cc_start: 0.6389 (tt) cc_final: 0.6156 (tt) outliers start: 12 outliers final: 12 residues processed: 66 average time/residue: 0.1580 time to fit residues: 14.8222 Evaluate side-chains 68 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 451 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 13 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 26 optimal weight: 0.0010 chunk 6 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.190488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.147075 restraints weight = 4677.936| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.33 r_work: 0.3429 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4013 Z= 0.119 Angle : 0.540 8.261 5477 Z= 0.259 Chirality : 0.037 0.125 642 Planarity : 0.004 0.043 680 Dihedral : 3.685 12.772 545 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.66 % Allowed : 10.90 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.38), residues: 510 helix: 1.46 (0.26), residues: 380 sheet: -1.96 (2.01), residues: 10 loop : 1.05 (0.60), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 50 HIS 0.001 0.000 HIS A 139 PHE 0.010 0.001 PHE A 201 TYR 0.017 0.001 TYR A 272 ARG 0.001 0.000 ARG A 402 Details of bonding type rmsd hydrogen bonds : bond 0.04229 ( 269) hydrogen bonds : angle 4.15361 ( 777) SS BOND : bond 0.00203 ( 2) SS BOND : angle 1.28793 ( 4) covalent geometry : bond 0.00268 ( 4011) covalent geometry : angle 0.53866 ( 5473) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.414 Fit side-chains REVERT: A 5 GLU cc_start: 0.7102 (pm20) cc_final: 0.6882 (pm20) REVERT: A 22 MET cc_start: 0.6773 (ttm) cc_final: 0.6458 (ptt) REVERT: A 56 ASN cc_start: 0.7227 (t0) cc_final: 0.6728 (t0) REVERT: A 166 ARG cc_start: 0.7616 (ttt180) cc_final: 0.6945 (tpp80) REVERT: A 293 LEU cc_start: 0.6318 (tt) cc_final: 0.6107 (tt) outliers start: 11 outliers final: 11 residues processed: 66 average time/residue: 0.1323 time to fit residues: 11.7821 Evaluate side-chains 66 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 451 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 39 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 50 optimal weight: 0.0170 chunk 26 optimal weight: 0.0470 chunk 1 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.190439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.146831 restraints weight = 4633.463| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.33 r_work: 0.3478 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4013 Z= 0.112 Angle : 0.524 7.609 5477 Z= 0.251 Chirality : 0.037 0.125 642 Planarity : 0.004 0.042 680 Dihedral : 3.598 12.077 545 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.66 % Allowed : 11.38 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.38), residues: 510 helix: 1.68 (0.27), residues: 374 sheet: -2.10 (1.91), residues: 10 loop : 0.96 (0.58), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 50 HIS 0.001 0.000 HIS A 139 PHE 0.010 0.001 PHE A 201 TYR 0.016 0.001 TYR A 272 ARG 0.002 0.000 ARG A 461 Details of bonding type rmsd hydrogen bonds : bond 0.04114 ( 269) hydrogen bonds : angle 4.08351 ( 777) SS BOND : bond 0.00182 ( 2) SS BOND : angle 1.22660 ( 4) covalent geometry : bond 0.00246 ( 4011) covalent geometry : angle 0.52272 ( 5473) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2536.01 seconds wall clock time: 45 minutes 34.57 seconds (2734.57 seconds total)