Starting phenix.real_space_refine on Thu Mar 6 07:08:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cdp_16592/03_2025/8cdp_16592.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cdp_16592/03_2025/8cdp_16592.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cdp_16592/03_2025/8cdp_16592.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cdp_16592/03_2025/8cdp_16592.map" model { file = "/net/cci-nas-00/data/ceres_data/8cdp_16592/03_2025/8cdp_16592.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cdp_16592/03_2025/8cdp_16592.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 3290 2.51 5 N 913 2.21 5 O 967 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 5200 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2472 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 17, 'TRANS': 295} Chain breaks: 1 Chain: "B" Number of atoms: 2728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2728 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 16, 'TRANS': 324} Chain breaks: 1 Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N ASP A 366 " occ=0.00 ... (6 atoms not shown) pdb=" OD2 ASP A 366 " occ=0.00 residue: pdb=" N ASP A 367 " occ=0.00 ... (6 atoms not shown) pdb=" OD2 ASP A 367 " occ=0.00 residue: pdb=" N MET B 317 " occ=0.00 ... (6 atoms not shown) pdb=" CE MET B 317 " occ=0.00 residue: pdb=" N ALA B 318 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA B 318 " occ=0.00 residue: pdb=" N ARG B 382 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG B 382 " occ=0.00 residue: pdb=" N ASP B 383 " occ=0.00 ... (6 atoms not shown) pdb=" OD2 ASP B 383 " occ=0.00 Time building chain proxies: 3.74, per 1000 atoms: 0.72 Number of scatterers: 5200 At special positions: 0 Unit cell: (62.37, 64.8, 122.31, 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 967 8.00 N 913 7.00 C 3290 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 622.8 milliseconds 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1246 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 5 sheets defined 28.0% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 196 through 217 removed outlier: 3.795A pdb=" N ARG A 200 " --> pdb=" O ASP A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 237 removed outlier: 3.711A pdb=" N MET A 237 " --> pdb=" O PRO A 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 234 through 237' Processing helix chain 'A' and resid 246 through 257 removed outlier: 3.648A pdb=" N VAL A 255 " --> pdb=" O GLN A 251 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ASN A 256 " --> pdb=" O ARG A 252 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N HIS A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 277 removed outlier: 4.688A pdb=" N LYS A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 359 removed outlier: 3.810A pdb=" N VAL A 353 " --> pdb=" O ARG A 349 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR A 359 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 438 removed outlier: 3.937A pdb=" N LYS A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALA A 438 " --> pdb=" O ASN A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 468 removed outlier: 3.639A pdb=" N VAL A 444 " --> pdb=" O ASP A 440 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N GLU A 461 " --> pdb=" O GLY A 457 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ASP A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 151 removed outlier: 3.564A pdb=" N ARG B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 235 Processing helix chain 'B' and resid 264 through 274 removed outlier: 4.101A pdb=" N GLN B 274 " --> pdb=" O HIS B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 298 removed outlier: 3.790A pdb=" N ALA B 289 " --> pdb=" O GLU B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 375 removed outlier: 3.523A pdb=" N ALA B 369 " --> pdb=" O LYS B 365 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU B 374 " --> pdb=" O ASP B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 476 removed outlier: 4.029A pdb=" N GLU B 476 " --> pdb=" O ALA B 472 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 156 through 161 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 156 through 161 current: chain 'A' and resid 259 through 263 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 263 current: chain 'A' and resid 304 through 309 removed outlier: 6.713A pdb=" N HIS A 306 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL A 318 " --> pdb=" O HIS A 306 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASP A 308 " --> pdb=" O LEU A 316 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 319 current: chain 'A' and resid 337 through 344 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 337 through 344 current: chain 'A' and resid 399 through 412 Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 172 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 186 through 192 current: chain 'B' and resid 174 through 179 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 174 through 179 current: chain 'B' and resid 319 through 326 removed outlier: 6.800A pdb=" N GLU B 324 " --> pdb=" O THR B 332 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS B 330 " --> pdb=" O ASN B 326 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 330 through 333 current: chain 'B' and resid 353 through 360 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 353 through 360 current: chain 'B' and resid 416 through 425 removed outlier: 6.310A pdb=" N THR B 416 " --> pdb=" O PRO B 446 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 243 through 245 Processing sheet with id=AA4, first strand: chain 'A' and resid 362 through 365 Processing sheet with id=AA5, first strand: chain 'B' and resid 378 through 380 150 hydrogen bonds defined for protein. 438 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: 1.27 Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1240 1.33 - 1.45: 1004 1.45 - 1.57: 3012 1.57 - 1.69: 0 1.69 - 1.81: 49 Bond restraints: 5305 Sorted by residual: bond pdb=" N ILE A 348 " pdb=" CA ILE A 348 " ideal model delta sigma weight residual 1.458 1.500 -0.043 1.27e-02 6.20e+03 1.14e+01 bond pdb=" N ARG A 350 " pdb=" CA ARG A 350 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.06e+00 bond pdb=" N VAL B 312 " pdb=" CA VAL B 312 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.11e-02 8.12e+03 6.04e+00 bond pdb=" C GLN A 351 " pdb=" O GLN A 351 " ideal model delta sigma weight residual 1.237 1.209 0.028 1.17e-02 7.31e+03 5.55e+00 bond pdb=" N VAL B 397 " pdb=" CA VAL B 397 " ideal model delta sigma weight residual 1.455 1.480 -0.025 1.06e-02 8.90e+03 5.50e+00 ... (remaining 5300 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 7071 2.74 - 5.49: 103 5.49 - 8.23: 11 8.23 - 10.97: 2 10.97 - 13.72: 2 Bond angle restraints: 7189 Sorted by residual: angle pdb=" CB GLU B 319 " pdb=" CG GLU B 319 " pdb=" CD GLU B 319 " ideal model delta sigma weight residual 112.60 126.32 -13.72 1.70e+00 3.46e-01 6.51e+01 angle pdb=" CB GLU A 354 " pdb=" CG GLU A 354 " pdb=" CD GLU A 354 " ideal model delta sigma weight residual 112.60 126.24 -13.64 1.70e+00 3.46e-01 6.44e+01 angle pdb=" C MET B 317 " pdb=" CA MET B 317 " pdb=" CB MET B 317 " ideal model delta sigma weight residual 116.63 110.43 6.20 1.16e+00 7.43e-01 2.86e+01 angle pdb=" N GLN A 351 " pdb=" CA GLN A 351 " pdb=" C GLN A 351 " ideal model delta sigma weight residual 111.28 105.71 5.57 1.09e+00 8.42e-01 2.61e+01 angle pdb=" CA ASP B 395 " pdb=" CB ASP B 395 " pdb=" CG ASP B 395 " ideal model delta sigma weight residual 112.60 117.64 -5.04 1.00e+00 1.00e+00 2.54e+01 ... (remaining 7184 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.95: 2942 15.95 - 31.90: 236 31.90 - 47.84: 44 47.84 - 63.79: 19 63.79 - 79.74: 6 Dihedral angle restraints: 3247 sinusoidal: 1330 harmonic: 1917 Sorted by residual: dihedral pdb=" CA LYS B 365 " pdb=" C LYS B 365 " pdb=" N LYS B 366 " pdb=" CA LYS B 366 " ideal model delta harmonic sigma weight residual 180.00 -156.95 -23.05 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA MET B 237 " pdb=" C MET B 237 " pdb=" N PRO B 238 " pdb=" CA PRO B 238 " ideal model delta harmonic sigma weight residual 180.00 159.97 20.03 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" C ARG B 315 " pdb=" N ARG B 315 " pdb=" CA ARG B 315 " pdb=" CB ARG B 315 " ideal model delta harmonic sigma weight residual -122.60 -112.69 -9.91 0 2.50e+00 1.60e-01 1.57e+01 ... (remaining 3244 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 677 0.059 - 0.119: 112 0.119 - 0.178: 7 0.178 - 0.238: 6 0.238 - 0.297: 2 Chirality restraints: 804 Sorted by residual: chirality pdb=" CA ARG B 315 " pdb=" N ARG B 315 " pdb=" C ARG B 315 " pdb=" CB ARG B 315 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CB VAL B 312 " pdb=" CA VAL B 312 " pdb=" CG1 VAL B 312 " pdb=" CG2 VAL B 312 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA VAL A 353 " pdb=" N VAL A 353 " pdb=" C VAL A 353 " pdb=" CB VAL A 353 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 801 not shown) Planarity restraints: 928 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 315 " -0.016 2.00e-02 2.50e+03 3.31e-02 1.09e+01 pdb=" C ARG B 315 " 0.057 2.00e-02 2.50e+03 pdb=" O ARG B 315 " -0.021 2.00e-02 2.50e+03 pdb=" N ARG B 316 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 346 " -0.014 2.00e-02 2.50e+03 2.65e-02 7.03e+00 pdb=" C PRO A 346 " 0.046 2.00e-02 2.50e+03 pdb=" O PRO A 346 " -0.017 2.00e-02 2.50e+03 pdb=" N PRO A 347 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 316 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.91e+00 pdb=" C ARG B 316 " -0.042 2.00e-02 2.50e+03 pdb=" O ARG B 316 " 0.016 2.00e-02 2.50e+03 pdb=" N MET B 317 " 0.015 2.00e-02 2.50e+03 ... (remaining 925 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 980 2.78 - 3.31: 5055 3.31 - 3.84: 8743 3.84 - 4.37: 9875 4.37 - 4.90: 16691 Nonbonded interactions: 41344 Sorted by model distance: nonbonded pdb=" OG SER B 309 " pdb=" OE2 GLU B 324 " model vdw 2.247 3.040 nonbonded pdb=" O SER A 235 " pdb=" NH1 ARG A 238 " model vdw 2.270 3.120 nonbonded pdb=" OD1 ASP A 462 " pdb=" NH2 ARG A 465 " model vdw 2.293 3.120 nonbonded pdb=" NZ LYS A 272 " pdb=" O LEU A 458 " model vdw 2.308 3.120 nonbonded pdb=" OG1 THR A 185 " pdb=" O ARG B 252 " model vdw 2.317 3.040 ... (remaining 41339 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 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: 1.600 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.420 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 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 : 0.003 0.043 5305 Z= 0.221 Angle : 0.783 13.716 7189 Z= 0.472 Chirality : 0.048 0.297 804 Planarity : 0.005 0.047 928 Dihedral : 12.956 79.740 2001 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.36 % Allowed : 0.53 % Favored : 99.11 % Cbeta Deviations : 0.16 % 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: 0.12 (0.33), residues: 646 helix: 2.13 (0.41), residues: 165 sheet: 0.65 (0.38), residues: 175 loop : -1.50 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 265 HIS 0.002 0.000 HIS A 332 PHE 0.011 0.001 PHE B 320 TYR 0.008 0.001 TYR B 251 ARG 0.020 0.001 ARG B 315 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 MET cc_start: 0.8835 (mtp) cc_final: 0.8616 (mtp) REVERT: A 224 TYR cc_start: 0.8829 (t80) cc_final: 0.8579 (t80) REVERT: B 223 MET cc_start: 0.8422 (mmp) cc_final: 0.8204 (mmp) REVERT: B 235 MET cc_start: 0.9138 (mmt) cc_final: 0.8837 (mpp) REVERT: B 237 MET cc_start: 0.8549 (mmm) cc_final: 0.8056 (mmm) outliers start: 2 outliers final: 0 residues processed: 56 average time/residue: 0.2218 time to fit residues: 16.5504 Evaluate side-chains 42 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 54 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 19 optimal weight: 0.1980 chunk 30 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 GLN ** 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 = 0.3318 r_free = 0.3318 target = 0.056788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.043094 restraints weight = 20055.523| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 4.33 r_work: 0.2814 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 5305 Z= 0.283 Angle : 0.620 6.671 7189 Z= 0.317 Chirality : 0.043 0.169 804 Planarity : 0.004 0.033 928 Dihedral : 4.847 20.727 717 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.53 % Allowed : 4.62 % Favored : 94.85 % 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: 0.04 (0.33), residues: 646 helix: 2.38 (0.41), residues: 156 sheet: 0.24 (0.36), residues: 195 loop : -1.48 (0.34), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 209 HIS 0.015 0.001 HIS B 275 PHE 0.017 0.002 PHE B 321 TYR 0.010 0.001 TYR A 203 ARG 0.005 0.000 ARG B 361 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.641 Fit side-chains revert: symmetry clash REVERT: A 224 TYR cc_start: 0.8972 (t80) cc_final: 0.8765 (t80) REVERT: B 219 MET cc_start: 0.8721 (tmm) cc_final: 0.8511 (tmm) REVERT: B 235 MET cc_start: 0.9378 (mmt) cc_final: 0.9043 (mpp) REVERT: B 237 MET cc_start: 0.8811 (mmm) cc_final: 0.8522 (mmm) REVERT: B 367 ARG cc_start: 0.9405 (ptp90) cc_final: 0.9052 (mtm110) outliers start: 3 outliers final: 3 residues processed: 46 average time/residue: 0.2121 time to fit residues: 12.5978 Evaluate side-chains 40 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain B residue 362 HIS Chi-restraints excluded: chain B residue 389 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 2 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 54 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 258 ASN ** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.053584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.039591 restraints weight = 20551.590| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 4.49 r_work: 0.2645 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 5305 Z= 0.418 Angle : 0.696 9.172 7189 Z= 0.351 Chirality : 0.044 0.168 804 Planarity : 0.004 0.034 928 Dihedral : 5.240 30.018 717 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.42 % Allowed : 7.99 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.47 (0.33), residues: 646 helix: 1.74 (0.40), residues: 158 sheet: -0.22 (0.39), residues: 177 loop : -1.48 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 407 HIS 0.011 0.001 HIS B 275 PHE 0.023 0.002 PHE B 225 TYR 0.015 0.002 TYR B 250 ARG 0.004 0.000 ARG B 361 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.618 Fit side-chains REVERT: A 216 ASN cc_start: 0.9309 (m110) cc_final: 0.9042 (p0) REVERT: A 224 TYR cc_start: 0.8960 (t80) cc_final: 0.8748 (t80) REVERT: B 219 MET cc_start: 0.8666 (tmm) cc_final: 0.8421 (tmm) REVERT: B 237 MET cc_start: 0.8852 (mmm) cc_final: 0.8555 (mmm) REVERT: B 315 ARG cc_start: 0.9355 (ttt90) cc_final: 0.8931 (ttm110) outliers start: 8 outliers final: 4 residues processed: 43 average time/residue: 0.1877 time to fit residues: 10.7718 Evaluate side-chains 42 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain B residue 362 HIS Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 393 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 41 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 0 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 15 optimal weight: 0.0670 chunk 52 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 328 GLN ** 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 = 0.3251 r_free = 0.3251 target = 0.056598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.041897 restraints weight = 19839.352| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 4.76 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5305 Z= 0.174 Angle : 0.571 9.378 7189 Z= 0.287 Chirality : 0.042 0.181 804 Planarity : 0.003 0.030 928 Dihedral : 4.816 26.688 717 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.89 % Allowed : 9.06 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.33), residues: 646 helix: 2.35 (0.41), residues: 156 sheet: 0.03 (0.37), residues: 195 loop : -1.51 (0.34), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 443 HIS 0.010 0.001 HIS B 275 PHE 0.009 0.001 PHE A 283 TYR 0.009 0.001 TYR A 203 ARG 0.003 0.000 ARG B 220 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.592 Fit side-chains revert: symmetry clash REVERT: A 152 MET cc_start: 0.7758 (ptt) cc_final: 0.6323 (pmm) REVERT: A 216 ASN cc_start: 0.9220 (m110) cc_final: 0.8933 (p0) REVERT: A 224 TYR cc_start: 0.8841 (t80) cc_final: 0.8461 (t80) REVERT: B 219 MET cc_start: 0.8438 (tmm) cc_final: 0.8073 (tmm) REVERT: B 237 MET cc_start: 0.8387 (mmm) cc_final: 0.8045 (mmm) REVERT: B 300 MET cc_start: 0.6132 (mmm) cc_final: 0.5796 (tpp) REVERT: B 315 ARG cc_start: 0.9306 (ttt90) cc_final: 0.8880 (ttm110) REVERT: B 393 LEU cc_start: 0.8865 (mt) cc_final: 0.8010 (mt) outliers start: 5 outliers final: 3 residues processed: 46 average time/residue: 0.1823 time to fit residues: 11.2891 Evaluate side-chains 45 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 362 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 8 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 chunk 12 optimal weight: 0.0050 chunk 0 optimal weight: 4.9990 chunk 47 optimal weight: 0.0060 chunk 58 optimal weight: 7.9990 chunk 7 optimal weight: 0.4980 overall best weight: 0.7012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 251 GLN ** 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 = 0.3249 r_free = 0.3249 target = 0.056332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.041814 restraints weight = 19741.860| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 4.75 r_work: 0.2688 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5305 Z= 0.164 Angle : 0.553 8.636 7189 Z= 0.275 Chirality : 0.042 0.167 804 Planarity : 0.003 0.030 928 Dihedral : 4.676 24.764 717 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.07 % Allowed : 11.01 % Favored : 87.92 % 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: -0.03 (0.33), residues: 646 helix: 2.47 (0.41), residues: 156 sheet: 0.05 (0.37), residues: 195 loop : -1.50 (0.34), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 443 HIS 0.009 0.001 HIS B 275 PHE 0.008 0.001 PHE A 227 TYR 0.012 0.001 TYR B 372 ARG 0.002 0.000 ARG A 350 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.7801 (ptt) cc_final: 0.6349 (pmm) REVERT: A 216 ASN cc_start: 0.9291 (m110) cc_final: 0.8993 (p0) REVERT: A 224 TYR cc_start: 0.8870 (t80) cc_final: 0.8537 (t80) REVERT: B 219 MET cc_start: 0.8611 (tmm) cc_final: 0.8204 (tmm) REVERT: B 237 MET cc_start: 0.8759 (mmm) cc_final: 0.8446 (mmm) outliers start: 6 outliers final: 5 residues processed: 45 average time/residue: 0.1752 time to fit residues: 10.6506 Evaluate side-chains 45 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain B residue 223 MET Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 362 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 61 optimal weight: 4.9990 chunk 10 optimal weight: 0.0000 chunk 26 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 47 optimal weight: 0.0570 chunk 54 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 62 optimal weight: 0.0970 overall best weight: 0.3300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.057189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.042650 restraints weight = 19783.332| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 4.79 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5305 Z= 0.140 Angle : 0.570 10.241 7189 Z= 0.274 Chirality : 0.043 0.327 804 Planarity : 0.003 0.029 928 Dihedral : 4.457 21.000 717 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.89 % Allowed : 12.08 % Favored : 87.03 % 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: 0.09 (0.33), residues: 646 helix: 2.59 (0.40), residues: 156 sheet: 0.06 (0.37), residues: 203 loop : -1.43 (0.34), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 407 HIS 0.007 0.001 HIS B 275 PHE 0.014 0.001 PHE B 321 TYR 0.009 0.001 TYR B 372 ARG 0.006 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.7725 (ptt) cc_final: 0.6315 (pmm) REVERT: A 216 ASN cc_start: 0.9195 (m110) cc_final: 0.8906 (p0) REVERT: A 224 TYR cc_start: 0.8809 (t80) cc_final: 0.8292 (t80) REVERT: B 219 MET cc_start: 0.8475 (tmm) cc_final: 0.8218 (tmm) REVERT: B 237 MET cc_start: 0.8419 (mmm) cc_final: 0.8055 (mmm) outliers start: 5 outliers final: 4 residues processed: 44 average time/residue: 0.1941 time to fit residues: 11.5110 Evaluate side-chains 45 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain B residue 362 HIS Chi-restraints excluded: chain B residue 389 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 18 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 48 optimal weight: 0.7980 chunk 2 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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 = 0.3200 r_free = 0.3200 target = 0.054530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.040057 restraints weight = 20114.649| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 4.71 r_work: 0.2628 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 5305 Z= 0.361 Angle : 0.660 11.685 7189 Z= 0.325 Chirality : 0.045 0.383 804 Planarity : 0.004 0.034 928 Dihedral : 4.882 20.923 717 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.42 % Allowed : 12.26 % Favored : 86.32 % 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: -0.26 (0.33), residues: 646 helix: 2.26 (0.41), residues: 154 sheet: -0.18 (0.37), residues: 208 loop : -1.56 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 407 HIS 0.005 0.001 HIS B 275 PHE 0.018 0.002 PHE B 225 TYR 0.014 0.002 TYR A 203 ARG 0.004 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.655 Fit side-chains revert: symmetry clash REVERT: A 152 MET cc_start: 0.7884 (ptt) cc_final: 0.6486 (pmm) REVERT: A 224 TYR cc_start: 0.8911 (t80) cc_final: 0.8602 (t80) REVERT: B 219 MET cc_start: 0.8659 (tmm) cc_final: 0.8196 (tmm) REVERT: B 315 ARG cc_start: 0.9366 (ttt90) cc_final: 0.8906 (ttm110) REVERT: B 320 PHE cc_start: 0.8546 (m-10) cc_final: 0.8318 (m-10) outliers start: 8 outliers final: 5 residues processed: 45 average time/residue: 0.1866 time to fit residues: 11.2489 Evaluate side-chains 43 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain B residue 223 MET Chi-restraints excluded: chain B residue 362 HIS Chi-restraints excluded: chain B residue 389 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 63 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN ** B 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.055575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.041289 restraints weight = 20014.354| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 4.72 r_work: 0.2682 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5305 Z= 0.172 Angle : 0.614 12.943 7189 Z= 0.289 Chirality : 0.043 0.352 804 Planarity : 0.003 0.038 928 Dihedral : 4.562 20.645 717 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.60 % Allowed : 12.61 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.15 (0.33), residues: 646 helix: 2.43 (0.41), residues: 155 sheet: -0.18 (0.37), residues: 205 loop : -1.49 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 443 HIS 0.006 0.001 HIS B 275 PHE 0.010 0.001 PHE B 321 TYR 0.012 0.001 TYR A 203 ARG 0.009 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.7781 (ptt) cc_final: 0.6436 (pmm) REVERT: A 216 ASN cc_start: 0.9279 (m110) cc_final: 0.9043 (p0) REVERT: A 224 TYR cc_start: 0.8911 (t80) cc_final: 0.8540 (t80) REVERT: B 219 MET cc_start: 0.8691 (tmm) cc_final: 0.8213 (tmm) REVERT: B 237 MET cc_start: 0.8876 (mmm) cc_final: 0.8651 (mmm) REVERT: B 315 ARG cc_start: 0.9315 (ttt90) cc_final: 0.8875 (ttm110) REVERT: B 320 PHE cc_start: 0.8545 (m-10) cc_final: 0.8276 (m-10) outliers start: 9 outliers final: 7 residues processed: 49 average time/residue: 0.1814 time to fit residues: 11.9566 Evaluate side-chains 48 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 362 HIS Chi-restraints excluded: chain B residue 389 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 52 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 7 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 9.9990 chunk 27 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN B 268 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.055695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.041354 restraints weight = 20122.693| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 4.77 r_work: 0.2689 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5305 Z= 0.168 Angle : 0.619 14.351 7189 Z= 0.295 Chirality : 0.044 0.377 804 Planarity : 0.003 0.029 928 Dihedral : 4.503 19.990 717 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.78 % Allowed : 13.32 % Favored : 84.90 % 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: -0.12 (0.33), residues: 646 helix: 2.42 (0.41), residues: 155 sheet: -0.16 (0.37), residues: 205 loop : -1.45 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 443 HIS 0.006 0.001 HIS B 275 PHE 0.008 0.001 PHE B 225 TYR 0.011 0.001 TYR A 203 ARG 0.008 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.566 Fit side-chains revert: symmetry clash REVERT: A 152 MET cc_start: 0.7765 (ptt) cc_final: 0.6414 (pmm) REVERT: A 216 ASN cc_start: 0.9308 (m110) cc_final: 0.9053 (p0) REVERT: A 224 TYR cc_start: 0.8837 (t80) cc_final: 0.8532 (t80) REVERT: B 219 MET cc_start: 0.8655 (tmm) cc_final: 0.8191 (tmm) REVERT: B 237 MET cc_start: 0.8822 (mmm) cc_final: 0.8580 (mmm) REVERT: B 315 ARG cc_start: 0.9323 (ttt90) cc_final: 0.8856 (ttm110) REVERT: B 320 PHE cc_start: 0.8518 (m-10) cc_final: 0.8248 (m-10) outliers start: 10 outliers final: 8 residues processed: 47 average time/residue: 0.1889 time to fit residues: 11.8388 Evaluate side-chains 48 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 223 MET Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 362 HIS Chi-restraints excluded: chain B residue 389 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 38 optimal weight: 1.9990 chunk 36 optimal weight: 0.0010 chunk 5 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 28 optimal weight: 0.3980 chunk 1 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.055956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.041507 restraints weight = 20013.456| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 4.76 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5305 Z= 0.187 Angle : 0.652 13.332 7189 Z= 0.311 Chirality : 0.043 0.290 804 Planarity : 0.003 0.033 928 Dihedral : 4.478 19.762 717 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.42 % Allowed : 13.85 % Favored : 84.72 % 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 (0.33), residues: 646 helix: 2.38 (0.40), residues: 155 sheet: -0.16 (0.36), residues: 205 loop : -1.41 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 407 HIS 0.006 0.001 HIS B 275 PHE 0.011 0.001 PHE B 321 TYR 0.011 0.001 TYR A 203 ARG 0.008 0.000 ARG B 367 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.571 Fit side-chains revert: symmetry clash REVERT: A 152 MET cc_start: 0.7706 (ptt) cc_final: 0.6405 (pmm) REVERT: A 216 ASN cc_start: 0.9203 (m110) cc_final: 0.8955 (p0) REVERT: A 224 TYR cc_start: 0.8802 (t80) cc_final: 0.8319 (t80) REVERT: B 219 MET cc_start: 0.8554 (tmm) cc_final: 0.8073 (tmm) REVERT: B 315 ARG cc_start: 0.9257 (ttt90) cc_final: 0.8805 (ttm110) REVERT: B 320 PHE cc_start: 0.8403 (m-10) cc_final: 0.8121 (m-10) outliers start: 8 outliers final: 8 residues processed: 47 average time/residue: 0.1780 time to fit residues: 11.2156 Evaluate side-chains 49 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 223 MET Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 362 HIS Chi-restraints excluded: chain B residue 389 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 27 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 0.2980 chunk 42 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 54 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.056313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.041721 restraints weight = 20149.309| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 4.82 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5305 Z= 0.170 Angle : 0.638 11.937 7189 Z= 0.307 Chirality : 0.042 0.160 804 Planarity : 0.004 0.060 928 Dihedral : 4.461 20.375 717 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.24 % Allowed : 14.21 % Favored : 84.55 % 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: -0.08 (0.33), residues: 646 helix: 2.33 (0.40), residues: 156 sheet: -0.16 (0.36), residues: 205 loop : -1.35 (0.35), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 407 HIS 0.006 0.001 HIS B 275 PHE 0.006 0.001 PHE B 225 TYR 0.011 0.001 TYR A 203 ARG 0.012 0.000 ARG A 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2712.87 seconds wall clock time: 47 minutes 22.29 seconds (2842.29 seconds total)