Starting phenix.real_space_refine on Sun Apr 27 01:29:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b1l_44083/04_2025/9b1l_44083.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b1l_44083/04_2025/9b1l_44083.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b1l_44083/04_2025/9b1l_44083.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b1l_44083/04_2025/9b1l_44083.map" model { file = "/net/cci-nas-00/data/ceres_data/9b1l_44083/04_2025/9b1l_44083.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b1l_44083/04_2025/9b1l_44083.cif" } resolution = 3.1 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= 0.027 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 2628 2.51 5 N 683 2.21 5 O 700 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 4041 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4029 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 31, 'TRANS': 497} 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: 3.54, per 1000 atoms: 0.88 Number of scatterers: 4041 At special positions: 0 Unit cell: (59.708, 90.86, 101.893, 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 700 8.00 N 683 7.00 C 2628 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: 1.07 Conformation dependent library (CDL) restraints added in 494.6 milliseconds 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 978 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 2 sheets defined 82.8% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 3 through 11 removed outlier: 3.601A pdb=" N LEU A 7 " --> pdb=" O PHE A 3 " (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: 3.520A pdb=" N SER A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 97 removed outlier: 3.955A pdb=" N ASP A 97 " --> pdb=" O GLN A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 105 removed outlier: 3.766A pdb=" N TRP A 105 " --> pdb=" O ALA A 102 " (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: 3.895A pdb=" N GLN A 146 " --> pdb=" O LYS A 142 " (cutoff:3.500A) Proline residue: A 162 - end of helix Processing helix chain 'A' and resid 168 through 189 removed outlier: 4.155A pdb=" N VAL A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE A 189 " --> pdb=" O THR A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 220 removed outlier: 3.611A pdb=" N ALA A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY A 209 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLY A 215 " --> pdb=" O MET A 211 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR A 216 " --> pdb=" O MET A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 252 removed outlier: 4.336A pdb=" N PHE A 238 " --> pdb=" O ASN A 234 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER A 239 " --> pdb=" O SER A 235 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY A 243 " --> pdb=" O SER A 239 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY A 251 " --> pdb=" O ALA A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 264 Processing helix chain 'A' and resid 264 through 274 removed outlier: 4.061A pdb=" N LEU A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N TRP A 274 " --> pdb=" O PHE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 286 Processing helix chain 'A' and resid 288 through 304 removed outlier: 4.198A pdb=" N GLN A 294 " --> pdb=" O ASP A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 311 removed outlier: 3.594A pdb=" N ALA A 308 " --> pdb=" O HIS A 305 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LYS A 309 " --> pdb=" O LYS A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 325 removed outlier: 6.245A pdb=" N GLU A 322 " --> pdb=" O SER A 318 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N GLU A 323 " --> pdb=" O SER A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 339 through 367 removed outlier: 4.528A pdb=" N PHE A 344 " --> pdb=" O PRO A 340 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N GLY A 362 " --> pdb=" O PHE A 358 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU A 365 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 371 removed outlier: 4.104A pdb=" N GLY A 371 " --> pdb=" O GLN A 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 368 through 371' Processing helix chain 'A' and resid 373 through 384 removed outlier: 3.895A pdb=" N ILE A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY A 382 " --> pdb=" O GLN A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 399 removed outlier: 3.906A pdb=" N ALA A 388 " --> pdb=" O VAL A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 419 removed outlier: 3.817A pdb=" N THR A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 425 No H-bonds generated for 'chain 'A' and resid 423 through 425' Processing helix chain 'A' and resid 426 through 455 removed outlier: 3.672A pdb=" N SER A 453 " --> pdb=" O THR A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 459 No H-bonds generated for 'chain 'A' and resid 457 through 459' Processing helix chain 'A' and resid 460 through 483 Proline residue: A 480 - end of helix removed outlier: 3.610A pdb=" N ARG A 483 " --> pdb=" O GLY A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 488 removed outlier: 3.648A pdb=" N VAL A 487 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 509 removed outlier: 4.506A pdb=" N LEU A 494 " --> pdb=" O PRO A 490 " (cutoff:3.500A) removed outlier: 3.598A 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 helix chain 'A' and resid 522 through 531 removed outlier: 3.521A pdb=" N VAL A 526 " --> pdb=" O THR A 522 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA A 530 " --> pdb=" O VAL A 526 " (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 86 through 88 271 hydrogen bonds defined for protein. 780 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: 1.13 Time building geometry restraints manager: 1.27 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: 1278 1.34 - 1.46: 964 1.46 - 1.58: 1854 1.58 - 1.70: 0 1.70 - 1.82: 47 Bond restraints: 4143 Sorted by residual: bond pdb=" C2 URC A 901 " pdb=" O11 URC A 901 " ideal model delta sigma weight residual 1.213 1.365 -0.152 2.00e-02 2.50e+03 5.78e+01 bond pdb=" C8 URC A 901 " pdb=" O24 URC A 901 " ideal model delta sigma weight residual 1.215 1.352 -0.137 2.00e-02 2.50e+03 4.67e+01 bond pdb=" C6 URC A 901 " pdb=" O13 URC A 901 " ideal model delta sigma weight residual 1.218 1.354 -0.136 2.00e-02 2.50e+03 4.65e+01 bond pdb=" C4 URC A 901 " pdb=" C5 URC A 901 " ideal model delta sigma weight residual 1.358 1.487 -0.129 2.00e-02 2.50e+03 4.18e+01 bond pdb=" C8 URC A 901 " pdb=" N7 URC A 901 " ideal model delta sigma weight residual 1.360 1.430 -0.070 2.00e-02 2.50e+03 1.21e+01 ... (remaining 4138 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 5583 2.66 - 5.32: 61 5.32 - 7.99: 5 7.99 - 10.65: 4 10.65 - 13.31: 3 Bond angle restraints: 5656 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 114.62 127.93 -13.31 3.00e+00 1.11e-01 1.97e+01 angle pdb=" C2 URC A 901 " pdb=" N1 URC A 901 " pdb=" C6 URC A 901 " ideal model delta sigma weight residual 129.31 117.43 11.88 3.00e+00 1.11e-01 1.57e+01 angle pdb=" N7 URC A 901 " pdb=" C8 URC A 901 " pdb=" N9 URC A 901 " ideal model delta sigma weight residual 104.73 116.29 -11.56 3.00e+00 1.11e-01 1.49e+01 angle pdb=" C5 URC A 901 " pdb=" C6 URC A 901 " pdb=" N1 URC A 901 " ideal model delta sigma weight residual 111.19 121.50 -10.31 3.00e+00 1.11e-01 1.18e+01 angle pdb=" N7 URC A 901 " pdb=" C8 URC A 901 " pdb=" O24 URC A 901 " ideal model delta sigma weight residual 129.09 119.59 9.50 3.00e+00 1.11e-01 1.00e+01 ... (remaining 5651 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 2292 17.32 - 34.65: 123 34.65 - 51.97: 19 51.97 - 69.29: 4 69.29 - 86.62: 2 Dihedral angle restraints: 2440 sinusoidal: 926 harmonic: 1514 Sorted by residual: dihedral pdb=" CG ARG A 401 " pdb=" CD ARG A 401 " pdb=" NE ARG A 401 " pdb=" CZ ARG A 401 " ideal model delta sinusoidal sigma weight residual -180.00 -137.90 -42.10 2 1.50e+01 4.44e-03 9.59e+00 dihedral pdb=" CB GLU A 278 " pdb=" CG GLU A 278 " pdb=" CD GLU A 278 " pdb=" OE1 GLU A 278 " ideal model delta sinusoidal sigma weight residual 0.00 -83.65 83.65 1 3.00e+01 1.11e-03 9.49e+00 dihedral pdb=" CA ASP A 335 " pdb=" C ASP A 335 " pdb=" N LEU A 336 " pdb=" CA LEU A 336 " ideal model delta harmonic sigma weight residual 180.00 165.35 14.65 0 5.00e+00 4.00e-02 8.59e+00 ... (remaining 2437 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 362 0.026 - 0.052: 204 0.052 - 0.078: 63 0.078 - 0.104: 27 0.104 - 0.130: 9 Chirality restraints: 665 Sorted by residual: chirality pdb=" CA PRO A 52 " pdb=" N PRO A 52 " pdb=" C PRO A 52 " pdb=" CB PRO A 52 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.25e-01 chirality pdb=" CA TYR A 272 " pdb=" N TYR A 272 " pdb=" C TYR A 272 " pdb=" CB TYR A 272 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 3.98e-01 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 2.60 0.12 2.00e-01 2.50e+01 3.65e-01 ... (remaining 662 not shown) Planarity restraints: 706 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 479 " 0.021 5.00e-02 4.00e+02 3.21e-02 1.65e+00 pdb=" N PRO A 480 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 480 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 480 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 297 " 0.006 2.00e-02 2.50e+03 1.21e-02 1.47e+00 pdb=" C ARG A 297 " -0.021 2.00e-02 2.50e+03 pdb=" O ARG A 297 " 0.008 2.00e-02 2.50e+03 pdb=" N LYS A 298 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 272 " 0.010 2.00e-02 2.50e+03 8.56e-03 1.46e+00 pdb=" CG TYR A 272 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR A 272 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR A 272 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 272 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 272 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 272 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 272 " 0.002 2.00e-02 2.50e+03 ... (remaining 703 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 1427 2.86 - 3.37: 4071 3.37 - 3.88: 6706 3.88 - 4.39: 7810 4.39 - 4.90: 12957 Nonbonded interactions: 32971 Sorted by model distance: nonbonded pdb=" OG SER A 239 " pdb=" OD2 ASP A 385 " model vdw 2.349 3.040 nonbonded pdb=" OE1 GLU A 220 " pdb=" OG SER A 279 " model vdw 2.398 3.040 nonbonded pdb=" O TRP A 30 " pdb=" OG1 THR A 33 " model vdw 2.408 3.040 nonbonded pdb=" OH TYR A 451 " pdb=" O PRO A 512 " model vdw 2.439 3.040 nonbonded pdb=" OD2 ASP A 385 " pdb=" NZ LYS A 389 " model vdw 2.489 3.120 ... (remaining 32966 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: 2.440 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.670 Find NCS groups from input model: 0.040 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 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 0.152 4145 Z= 0.308 Angle : 0.790 13.310 5660 Z= 0.389 Chirality : 0.038 0.130 665 Planarity : 0.005 0.032 706 Dihedral : 11.089 86.615 1456 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 0.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % 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: 0.53 (0.37), residues: 527 helix: 0.17 (0.27), residues: 366 sheet: None (None), residues: 0 loop : 1.27 (0.53), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 353 HIS 0.003 0.001 HIS A 83 PHE 0.013 0.002 PHE A 358 TYR 0.021 0.002 TYR A 272 ARG 0.005 0.001 ARG A 343 Details of bonding type rmsd hydrogen bonds : bond 0.11992 ( 271) hydrogen bonds : angle 5.46583 ( 780) SS BOND : bond 0.00137 ( 2) SS BOND : angle 2.28844 ( 4) covalent geometry : bond 0.00628 ( 4143) covalent geometry : angle 0.78753 ( 5656) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: A 166 ARG cc_start: 0.7530 (ttt180) cc_final: 0.7323 (ttt90) REVERT: A 332 SER cc_start: 0.7736 (t) cc_final: 0.7193 (p) REVERT: A 335 ASP cc_start: 0.5566 (m-30) cc_final: 0.5218 (m-30) REVERT: A 340 PRO cc_start: 0.8075 (Cg_exo) cc_final: 0.7812 (Cg_endo) REVERT: A 349 SER cc_start: 0.7614 (t) cc_final: 0.7403 (p) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1657 time to fit residues: 16.7456 Evaluate side-chains 52 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 26 optimal weight: 0.0770 chunk 40 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 24 optimal weight: 0.4980 chunk 30 optimal weight: 0.0060 chunk 47 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 overall best weight: 0.4354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 515 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.181853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.143649 restraints weight = 4439.008| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.01 r_work: 0.3550 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4145 Z= 0.129 Angle : 0.529 5.211 5660 Z= 0.270 Chirality : 0.039 0.124 665 Planarity : 0.004 0.035 706 Dihedral : 4.091 13.534 562 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.40 % Allowed : 8.39 % Favored : 90.21 % 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: 1.35 (0.37), residues: 527 helix: 0.89 (0.27), residues: 382 sheet: None (None), residues: 0 loop : 1.33 (0.52), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.002 0.001 HIS A 139 PHE 0.011 0.001 PHE A 16 TYR 0.020 0.002 TYR A 272 ARG 0.003 0.000 ARG A 461 Details of bonding type rmsd hydrogen bonds : bond 0.04939 ( 271) hydrogen bonds : angle 4.19504 ( 780) SS BOND : bond 0.00102 ( 2) SS BOND : angle 1.66685 ( 4) covalent geometry : bond 0.00283 ( 4143) covalent geometry : angle 0.52762 ( 5656) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.431 Fit side-chains REVERT: A 146 GLN cc_start: 0.7655 (mt0) cc_final: 0.6997 (tp-100) REVERT: A 332 SER cc_start: 0.7835 (t) cc_final: 0.7135 (p) REVERT: A 335 ASP cc_start: 0.5623 (m-30) cc_final: 0.5294 (m-30) REVERT: A 377 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7589 (mp) REVERT: A 513 GLU cc_start: 0.8305 (tp30) cc_final: 0.8088 (tp30) outliers start: 6 outliers final: 4 residues processed: 65 average time/residue: 0.1391 time to fit residues: 11.8446 Evaluate side-chains 52 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 448 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 7 optimal weight: 0.3980 chunk 10 optimal weight: 0.0030 chunk 6 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 30 optimal weight: 0.0270 chunk 8 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 overall best weight: 0.4450 ------------------------------------------------------------------------------- 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 = 0.4066 r_free = 0.4066 target = 0.181700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.143042 restraints weight = 4415.353| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.03 r_work: 0.3546 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4145 Z= 0.117 Angle : 0.485 5.454 5660 Z= 0.246 Chirality : 0.037 0.119 665 Planarity : 0.004 0.036 706 Dihedral : 3.851 12.326 562 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.40 % Allowed : 10.26 % Favored : 88.34 % 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: 1.66 (0.37), residues: 527 helix: 1.22 (0.27), residues: 380 sheet: -1.45 (1.52), residues: 10 loop : 1.36 (0.55), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.002 0.000 HIS A 139 PHE 0.013 0.001 PHE A 88 TYR 0.019 0.002 TYR A 272 ARG 0.001 0.000 ARG A 345 Details of bonding type rmsd hydrogen bonds : bond 0.04598 ( 271) hydrogen bonds : angle 3.99454 ( 780) SS BOND : bond 0.00109 ( 2) SS BOND : angle 1.55570 ( 4) covalent geometry : bond 0.00250 ( 4143) covalent geometry : angle 0.48365 ( 5656) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.443 Fit side-chains revert: symmetry clash REVERT: A 146 GLN cc_start: 0.7657 (mt0) cc_final: 0.6966 (tp-100) REVERT: A 332 SER cc_start: 0.7794 (t) cc_final: 0.7049 (p) REVERT: A 335 ASP cc_start: 0.5538 (m-30) cc_final: 0.5188 (m-30) REVERT: A 377 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7543 (mp) outliers start: 6 outliers final: 5 residues processed: 56 average time/residue: 0.1496 time to fit residues: 11.2595 Evaluate side-chains 54 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 448 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 16 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3941 r_free = 0.3941 target = 0.173212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.134330 restraints weight = 4476.750| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.05 r_work: 0.3398 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4145 Z= 0.151 Angle : 0.514 5.508 5660 Z= 0.257 Chirality : 0.038 0.119 665 Planarity : 0.004 0.035 706 Dihedral : 3.906 12.371 562 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 2.80 % Allowed : 9.32 % Favored : 87.88 % 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: 1.63 (0.37), residues: 527 helix: 1.23 (0.27), residues: 380 sheet: -1.76 (1.56), residues: 10 loop : 1.25 (0.57), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 353 HIS 0.002 0.001 HIS A 47 PHE 0.011 0.001 PHE A 358 TYR 0.021 0.002 TYR A 272 ARG 0.002 0.000 ARG A 227 Details of bonding type rmsd hydrogen bonds : bond 0.04955 ( 271) hydrogen bonds : angle 4.08025 ( 780) SS BOND : bond 0.00154 ( 2) SS BOND : angle 1.52060 ( 4) covalent geometry : bond 0.00358 ( 4143) covalent geometry : angle 0.51273 ( 5656) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: A 377 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.7104 (mp) outliers start: 12 outliers final: 6 residues processed: 52 average time/residue: 0.1277 time to fit residues: 9.0469 Evaluate side-chains 50 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 482 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 25 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 24 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3924 r_free = 0.3924 target = 0.171208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.132552 restraints weight = 4497.283| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.07 r_work: 0.3402 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4145 Z= 0.136 Angle : 0.495 5.505 5660 Z= 0.247 Chirality : 0.037 0.118 665 Planarity : 0.004 0.035 706 Dihedral : 3.793 12.019 562 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 2.56 % Allowed : 10.26 % Favored : 87.18 % 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: 527 helix: 1.34 (0.27), residues: 380 sheet: -1.87 (1.66), residues: 10 loop : 1.26 (0.57), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.002 0.001 HIS A 47 PHE 0.011 0.001 PHE A 358 TYR 0.020 0.002 TYR A 272 ARG 0.001 0.000 ARG A 345 Details of bonding type rmsd hydrogen bonds : bond 0.04700 ( 271) hydrogen bonds : angle 4.02820 ( 780) SS BOND : bond 0.00162 ( 2) SS BOND : angle 1.39003 ( 4) covalent geometry : bond 0.00319 ( 4143) covalent geometry : angle 0.49355 ( 5656) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.435 Fit side-chains REVERT: A 377 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.7158 (mp) outliers start: 11 outliers final: 6 residues processed: 50 average time/residue: 0.1390 time to fit residues: 9.5594 Evaluate side-chains 49 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 482 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 35 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 48 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3928 r_free = 0.3928 target = 0.171564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.133150 restraints weight = 4407.183| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.04 r_work: 0.3411 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4145 Z= 0.128 Angle : 0.482 5.535 5660 Z= 0.241 Chirality : 0.037 0.119 665 Planarity : 0.004 0.035 706 Dihedral : 3.709 11.973 562 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 2.56 % Allowed : 10.49 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.38), residues: 527 helix: 1.41 (0.27), residues: 381 sheet: -1.71 (1.85), residues: 10 loop : 1.26 (0.58), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.002 0.001 HIS A 47 PHE 0.011 0.001 PHE A 358 TYR 0.019 0.002 TYR A 272 ARG 0.001 0.000 ARG A 169 Details of bonding type rmsd hydrogen bonds : bond 0.04521 ( 271) hydrogen bonds : angle 3.95532 ( 780) SS BOND : bond 0.00145 ( 2) SS BOND : angle 1.31033 ( 4) covalent geometry : bond 0.00295 ( 4143) covalent geometry : angle 0.48137 ( 5656) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: A 377 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.7033 (mp) outliers start: 11 outliers final: 9 residues processed: 54 average time/residue: 0.1195 time to fit residues: 8.8373 Evaluate side-chains 55 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 482 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 7 optimal weight: 0.3980 chunk 47 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 0.0050 chunk 26 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 8 optimal weight: 0.4980 overall best weight: 0.5194 ------------------------------------------------------------------------------- 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 = 0.3948 r_free = 0.3948 target = 0.173867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.135316 restraints weight = 4492.418| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.09 r_work: 0.3420 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4145 Z= 0.117 Angle : 0.471 5.530 5660 Z= 0.233 Chirality : 0.036 0.119 665 Planarity : 0.004 0.035 706 Dihedral : 3.592 11.536 562 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 2.33 % Allowed : 11.42 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.38), residues: 527 helix: 1.54 (0.27), residues: 381 sheet: -1.72 (1.85), residues: 10 loop : 1.28 (0.58), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.002 0.000 HIS A 47 PHE 0.010 0.001 PHE A 361 TYR 0.018 0.001 TYR A 272 ARG 0.002 0.000 ARG A 169 Details of bonding type rmsd hydrogen bonds : bond 0.04250 ( 271) hydrogen bonds : angle 3.86647 ( 780) SS BOND : bond 0.00132 ( 2) SS BOND : angle 1.24157 ( 4) covalent geometry : bond 0.00261 ( 4143) covalent geometry : angle 0.46966 ( 5656) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.463 Fit side-chains revert: symmetry clash REVERT: A 377 LEU cc_start: 0.7236 (OUTLIER) cc_final: 0.6991 (mp) REVERT: A 438 LEU cc_start: 0.7392 (OUTLIER) cc_final: 0.7158 (tt) outliers start: 10 outliers final: 6 residues processed: 50 average time/residue: 0.1752 time to fit residues: 12.0636 Evaluate side-chains 52 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 482 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 37 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 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 = 0.3950 r_free = 0.3950 target = 0.174356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.135354 restraints weight = 4400.806| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.05 r_work: 0.3410 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4145 Z= 0.132 Angle : 0.494 5.945 5660 Z= 0.242 Chirality : 0.037 0.118 665 Planarity : 0.004 0.035 706 Dihedral : 3.639 11.845 562 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 2.10 % Allowed : 11.89 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.38), residues: 527 helix: 1.50 (0.27), residues: 381 sheet: -1.92 (1.76), residues: 10 loop : 1.35 (0.59), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 353 HIS 0.002 0.001 HIS A 47 PHE 0.011 0.001 PHE A 361 TYR 0.020 0.002 TYR A 272 ARG 0.002 0.000 ARG A 169 Details of bonding type rmsd hydrogen bonds : bond 0.04481 ( 271) hydrogen bonds : angle 3.91235 ( 780) SS BOND : bond 0.00161 ( 2) SS BOND : angle 1.26498 ( 4) covalent geometry : bond 0.00311 ( 4143) covalent geometry : angle 0.49330 ( 5656) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: A 377 LEU cc_start: 0.7176 (OUTLIER) cc_final: 0.6906 (mp) outliers start: 9 outliers final: 8 residues processed: 52 average time/residue: 0.1332 time to fit residues: 9.4190 Evaluate side-chains 51 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 482 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 27 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 49 optimal weight: 0.0980 chunk 48 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.174210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.135421 restraints weight = 4510.287| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.06 r_work: 0.3414 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4145 Z= 0.122 Angle : 0.494 8.821 5660 Z= 0.240 Chirality : 0.037 0.131 665 Planarity : 0.004 0.035 706 Dihedral : 3.588 11.641 562 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 2.33 % Allowed : 11.42 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.38), residues: 527 helix: 1.56 (0.27), residues: 381 sheet: -2.04 (1.75), residues: 10 loop : 1.39 (0.60), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.002 0.000 HIS A 47 PHE 0.011 0.001 PHE A 361 TYR 0.019 0.002 TYR A 272 ARG 0.001 0.000 ARG A 169 Details of bonding type rmsd hydrogen bonds : bond 0.04317 ( 271) hydrogen bonds : angle 3.88224 ( 780) SS BOND : bond 0.00150 ( 2) SS BOND : angle 1.22076 ( 4) covalent geometry : bond 0.00278 ( 4143) covalent geometry : angle 0.49318 ( 5656) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: A 377 LEU cc_start: 0.7154 (OUTLIER) cc_final: 0.6889 (mp) REVERT: A 438 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.7076 (tt) outliers start: 10 outliers final: 8 residues processed: 50 average time/residue: 0.1422 time to fit residues: 9.7598 Evaluate side-chains 51 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 482 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 40 optimal weight: 0.5980 chunk 5 optimal weight: 4.9990 chunk 6 optimal weight: 0.4980 chunk 39 optimal weight: 0.4980 chunk 33 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 26 optimal weight: 0.1980 chunk 50 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.175017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.136197 restraints weight = 4443.118| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.04 r_work: 0.3423 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4145 Z= 0.116 Angle : 0.479 5.866 5660 Z= 0.234 Chirality : 0.037 0.120 665 Planarity : 0.004 0.036 706 Dihedral : 3.528 11.480 562 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 2.33 % Allowed : 11.42 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.38), residues: 527 helix: 1.61 (0.27), residues: 381 sheet: -2.00 (1.76), residues: 10 loop : 1.38 (0.60), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.002 0.000 HIS A 47 PHE 0.010 0.001 PHE A 361 TYR 0.018 0.001 TYR A 272 ARG 0.001 0.000 ARG A 461 Details of bonding type rmsd hydrogen bonds : bond 0.04198 ( 271) hydrogen bonds : angle 3.83807 ( 780) SS BOND : bond 0.00135 ( 2) SS BOND : angle 1.17860 ( 4) covalent geometry : bond 0.00261 ( 4143) covalent geometry : angle 0.47767 ( 5656) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: A 120 ASP cc_start: 0.7996 (t70) cc_final: 0.7388 (t0) REVERT: A 377 LEU cc_start: 0.7047 (OUTLIER) cc_final: 0.6783 (mp) REVERT: A 438 LEU cc_start: 0.7303 (OUTLIER) cc_final: 0.7076 (tt) outliers start: 10 outliers final: 7 residues processed: 53 average time/residue: 0.1358 time to fit residues: 9.8951 Evaluate side-chains 52 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 482 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 23 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 3 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.173685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.135363 restraints weight = 4445.160| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.02 r_work: 0.3413 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4145 Z= 0.131 Angle : 0.493 5.912 5660 Z= 0.241 Chirality : 0.037 0.119 665 Planarity : 0.004 0.036 706 Dihedral : 3.592 11.671 562 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 2.33 % Allowed : 12.12 % Favored : 85.55 % 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: 2.05 (0.38), residues: 527 helix: 1.55 (0.27), residues: 381 sheet: -2.00 (1.76), residues: 10 loop : 1.41 (0.60), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 353 HIS 0.002 0.001 HIS A 47 PHE 0.011 0.001 PHE A 361 TYR 0.020 0.002 TYR A 272 ARG 0.001 0.000 ARG A 461 Details of bonding type rmsd hydrogen bonds : bond 0.04429 ( 271) hydrogen bonds : angle 3.89197 ( 780) SS BOND : bond 0.00166 ( 2) SS BOND : angle 1.23930 ( 4) covalent geometry : bond 0.00305 ( 4143) covalent geometry : angle 0.49217 ( 5656) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3933.46 seconds wall clock time: 70 minutes 12.10 seconds (4212.10 seconds total)