Starting phenix.real_space_refine on Sun Mar 10 21:22:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cdp_16592/03_2024/8cdp_16592.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cdp_16592/03_2024/8cdp_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cdp_16592/03_2024/8cdp_16592.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cdp_16592/03_2024/8cdp_16592.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cdp_16592/03_2024/8cdp_16592.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cdp_16592/03_2024/8cdp_16592.pdb" } 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 Residue "B PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 3.28, per 1000 atoms: 0.63 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 - 3.50 Amino acid : False - 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: 1.58 Conformation dependent library (CDL) restraints added in 864.9 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: 0.57 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: 1.15 Time building geometry restraints manager: 1.76 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: 99.72 - 106.57: 186 106.57 - 113.43: 2894 113.43 - 120.28: 1843 120.28 - 127.13: 2198 127.13 - 133.99: 68 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 2.440 nonbonded pdb=" O SER A 235 " pdb=" NH1 ARG A 238 " model vdw 2.270 2.520 nonbonded pdb=" OD1 ASP A 462 " pdb=" NH2 ARG A 465 " model vdw 2.293 2.520 nonbonded pdb=" NZ LYS A 272 " pdb=" O LEU A 458 " model vdw 2.308 2.520 nonbonded pdb=" OG1 THR A 185 " pdb=" O ARG B 252 " model vdw 2.317 2.440 ... (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 ========== 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: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.690 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 17.750 Find NCS groups from input model: 0.160 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.860 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 0.643 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: 0.1857 time to fit residues: 13.6840 Evaluate side-chains 42 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.633 ------------------------------------------------------------------------------- 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: 10.0000 chunk 49 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 33 optimal weight: 0.0470 chunk 26 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 overall best weight: 1.3482 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5305 Z= 0.228 Angle : 0.580 6.487 7189 Z= 0.297 Chirality : 0.041 0.143 804 Planarity : 0.003 0.033 928 Dihedral : 4.743 20.403 717 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.71 % Allowed : 4.97 % Favored : 94.32 % 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: 0.08 (0.33), residues: 646 helix: 2.27 (0.41), residues: 161 sheet: 0.47 (0.38), residues: 185 loop : -1.53 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 209 HIS 0.012 0.001 HIS B 275 PHE 0.014 0.001 PHE B 321 TYR 0.010 0.001 TYR A 203 ARG 0.005 0.000 ARG B 315 *********************** 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 49 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 45 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: A 219 MET cc_start: 0.8853 (mtp) cc_final: 0.8634 (mtp) REVERT: A 224 TYR cc_start: 0.8721 (t80) cc_final: 0.8507 (t80) REVERT: A 302 LYS cc_start: 0.9298 (mmtp) cc_final: 0.9074 (mmtm) REVERT: B 219 MET cc_start: 0.8418 (tmm) cc_final: 0.8167 (tmm) REVERT: B 235 MET cc_start: 0.9157 (mmt) cc_final: 0.8901 (mpp) REVERT: B 237 MET cc_start: 0.8269 (mmm) cc_final: 0.8037 (mmm) REVERT: B 367 ARG cc_start: 0.9321 (ptp90) cc_final: 0.8930 (mtm110) outliers start: 4 outliers final: 3 residues processed: 47 average time/residue: 0.2038 time to fit residues: 12.5966 Evaluate side-chains 42 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 39 time to evaluate : 0.668 ------------------------------------------------------------------------------- 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 32 optimal weight: 0.1980 chunk 18 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 5305 Z= 0.371 Angle : 0.655 8.573 7189 Z= 0.332 Chirality : 0.043 0.135 804 Planarity : 0.004 0.036 928 Dihedral : 5.160 28.111 717 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.60 % Allowed : 7.82 % Favored : 90.59 % 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: -0.28 (0.33), residues: 646 helix: 1.67 (0.40), residues: 161 sheet: 0.14 (0.38), residues: 189 loop : -1.49 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 443 HIS 0.008 0.001 HIS B 275 PHE 0.022 0.002 PHE B 225 TYR 0.015 0.002 TYR B 250 ARG 0.005 0.000 ARG B 367 *********************** 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 52 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 43 time to evaluate : 0.642 Fit side-chains revert: symmetry clash REVERT: A 216 ASN cc_start: 0.9204 (m110) cc_final: 0.8911 (p0) REVERT: A 302 LYS cc_start: 0.9339 (mmtp) cc_final: 0.9137 (mmtm) REVERT: B 237 MET cc_start: 0.8214 (mmm) cc_final: 0.7979 (mmm) REVERT: B 315 ARG cc_start: 0.9294 (ttt90) cc_final: 0.8870 (ttm110) REVERT: B 334 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7593 (mmm) outliers start: 9 outliers final: 4 residues processed: 46 average time/residue: 0.1937 time to fit residues: 11.9161 Evaluate side-chains 45 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 40 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 334 MET 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 58 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5305 Z= 0.248 Angle : 0.579 7.804 7189 Z= 0.292 Chirality : 0.042 0.142 804 Planarity : 0.003 0.033 928 Dihedral : 4.883 21.715 717 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.60 % Allowed : 9.77 % Favored : 88.63 % 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: -0.19 (0.33), residues: 646 helix: 1.90 (0.40), residues: 161 sheet: 0.24 (0.38), residues: 185 loop : -1.54 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 443 HIS 0.006 0.001 HIS B 275 PHE 0.012 0.001 PHE B 225 TYR 0.021 0.002 TYR A 224 ARG 0.002 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 51 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 42 time to evaluate : 0.631 Fit side-chains revert: symmetry clash REVERT: A 152 MET cc_start: 0.7771 (ptt) cc_final: 0.6356 (pmm) REVERT: A 216 ASN cc_start: 0.9184 (m110) cc_final: 0.8914 (p0) REVERT: B 237 MET cc_start: 0.8185 (mmm) cc_final: 0.7959 (mmm) REVERT: B 315 ARG cc_start: 0.9273 (ttt90) cc_final: 0.8848 (ttm110) REVERT: B 334 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.7474 (mmm) outliers start: 9 outliers final: 4 residues processed: 45 average time/residue: 0.1880 time to fit residues: 11.3153 Evaluate side-chains 44 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 362 HIS Chi-restraints excluded: chain B residue 393 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 52 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 56 optimal weight: 0.0970 chunk 15 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5305 Z= 0.225 Angle : 0.583 7.567 7189 Z= 0.290 Chirality : 0.042 0.150 804 Planarity : 0.003 0.033 928 Dihedral : 4.772 21.690 717 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.78 % Allowed : 11.01 % Favored : 87.21 % 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: -0.20 (0.33), residues: 646 helix: 1.98 (0.40), residues: 161 sheet: 0.12 (0.38), residues: 192 loop : -1.56 (0.34), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 407 HIS 0.005 0.001 HIS B 275 PHE 0.012 0.001 PHE B 225 TYR 0.015 0.001 TYR A 224 ARG 0.002 0.000 ARG B 220 *********************** 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 53 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 43 time to evaluate : 0.662 Fit side-chains revert: symmetry clash REVERT: A 152 MET cc_start: 0.7785 (ptt) cc_final: 0.6365 (pmm) REVERT: A 216 ASN cc_start: 0.9182 (m110) cc_final: 0.8918 (p0) REVERT: A 224 TYR cc_start: 0.8556 (t80) cc_final: 0.8263 (t80) REVERT: A 302 LYS cc_start: 0.9343 (mmtp) cc_final: 0.9136 (mmtm) REVERT: B 237 MET cc_start: 0.8117 (mmm) cc_final: 0.7899 (mmm) REVERT: B 315 ARG cc_start: 0.9257 (ttt90) cc_final: 0.8830 (ttm110) REVERT: B 334 MET cc_start: 0.7744 (OUTLIER) cc_final: 0.7232 (mmm) outliers start: 10 outliers final: 7 residues processed: 49 average time/residue: 0.1819 time to fit residues: 12.0213 Evaluate side-chains 49 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 41 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 236 ASN 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 56 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 52 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN ** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5305 Z= 0.244 Angle : 0.593 9.205 7189 Z= 0.293 Chirality : 0.042 0.265 804 Planarity : 0.003 0.033 928 Dihedral : 4.739 21.852 717 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.95 % Allowed : 11.19 % Favored : 86.86 % 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: -0.25 (0.33), residues: 646 helix: 1.92 (0.40), residues: 161 sheet: 0.10 (0.38), residues: 192 loop : -1.58 (0.34), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 407 HIS 0.005 0.001 HIS B 275 PHE 0.009 0.001 PHE B 225 TYR 0.012 0.001 TYR A 224 ARG 0.002 0.000 ARG B 315 *********************** 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 55 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 44 time to evaluate : 0.674 Fit side-chains revert: symmetry clash REVERT: A 152 MET cc_start: 0.7787 (ptt) cc_final: 0.6405 (pmm) REVERT: A 216 ASN cc_start: 0.9171 (m110) cc_final: 0.8920 (p0) REVERT: A 224 TYR cc_start: 0.8542 (t80) cc_final: 0.8272 (t80) REVERT: A 302 LYS cc_start: 0.9343 (mmtp) cc_final: 0.9127 (mmtm) REVERT: B 315 ARG cc_start: 0.9276 (ttt90) cc_final: 0.8846 (ttm110) outliers start: 11 outliers final: 9 residues processed: 51 average time/residue: 0.1721 time to fit residues: 11.8196 Evaluate side-chains 51 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 42 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 362 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 7 optimal weight: 0.0370 chunk 35 optimal weight: 0.0060 chunk 45 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 chunk 39 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN ** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1841 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= 0.148 Angle : 0.580 13.717 7189 Z= 0.281 Chirality : 0.044 0.374 804 Planarity : 0.003 0.031 928 Dihedral : 4.552 21.198 717 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.78 % Allowed : 12.79 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.33), residues: 646 helix: 2.10 (0.40), residues: 161 sheet: 0.06 (0.37), residues: 201 loop : -1.49 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 443 HIS 0.005 0.001 HIS B 275 PHE 0.011 0.001 PHE B 321 TYR 0.012 0.001 TYR A 224 ARG 0.002 0.000 ARG B 220 *********************** 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 57 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 47 time to evaluate : 0.641 Fit side-chains revert: symmetry clash REVERT: A 152 MET cc_start: 0.7734 (ptt) cc_final: 0.6395 (pmm) REVERT: A 216 ASN cc_start: 0.9136 (m110) cc_final: 0.8892 (p0) REVERT: A 224 TYR cc_start: 0.8502 (t80) cc_final: 0.8234 (t80) REVERT: A 302 LYS cc_start: 0.9319 (mmtp) cc_final: 0.9104 (mmtm) REVERT: B 237 MET cc_start: 0.8266 (mmm) cc_final: 0.8064 (mmm) REVERT: B 315 ARG cc_start: 0.9251 (ttt90) cc_final: 0.8828 (ttm110) REVERT: B 321 PHE cc_start: 0.8536 (m-80) cc_final: 0.8305 (m-80) REVERT: B 367 ARG cc_start: 0.9303 (ptp90) cc_final: 0.9008 (ptt-90) outliers start: 10 outliers final: 8 residues processed: 55 average time/residue: 0.1778 time to fit residues: 13.0139 Evaluate side-chains 52 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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 265 LEU Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 362 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 12 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 42 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN ** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5305 Z= 0.232 Angle : 0.608 13.993 7189 Z= 0.292 Chirality : 0.043 0.357 804 Planarity : 0.003 0.032 928 Dihedral : 4.576 21.220 717 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.95 % Allowed : 12.08 % Favored : 85.97 % 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: 2.22 (0.41), residues: 161 sheet: 0.03 (0.37), residues: 201 loop : -1.49 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 443 HIS 0.004 0.001 HIS B 275 PHE 0.009 0.001 PHE B 225 TYR 0.010 0.001 TYR A 224 ARG 0.003 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 55 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 44 time to evaluate : 0.652 Fit side-chains REVERT: A 152 MET cc_start: 0.7736 (ptt) cc_final: 0.6389 (pmm) REVERT: A 216 ASN cc_start: 0.9162 (m110) cc_final: 0.8924 (p0) REVERT: A 224 TYR cc_start: 0.8533 (t80) cc_final: 0.8303 (t80) REVERT: A 302 LYS cc_start: 0.9329 (mmtp) cc_final: 0.9114 (mmtm) REVERT: B 315 ARG cc_start: 0.9260 (ttt90) cc_final: 0.8826 (ttm110) REVERT: B 321 PHE cc_start: 0.8566 (m-80) cc_final: 0.8309 (m-80) REVERT: B 367 ARG cc_start: 0.9319 (ptp90) cc_final: 0.9045 (ptt-90) outliers start: 11 outliers final: 9 residues processed: 53 average time/residue: 0.1798 time to fit residues: 12.7373 Evaluate side-chains 52 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 43 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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 265 LEU Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 362 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 25 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 55 optimal weight: 0.3980 chunk 58 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN ** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5305 Z= 0.221 Angle : 0.619 13.196 7189 Z= 0.300 Chirality : 0.043 0.318 804 Planarity : 0.003 0.032 928 Dihedral : 4.596 21.091 717 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.95 % Allowed : 12.79 % Favored : 85.26 % 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: -0.19 (0.33), residues: 646 helix: 2.08 (0.41), residues: 162 sheet: -0.00 (0.37), residues: 201 loop : -1.57 (0.34), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 443 HIS 0.004 0.001 HIS B 275 PHE 0.010 0.001 PHE B 225 TYR 0.010 0.001 TYR A 224 ARG 0.003 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 56 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 45 time to evaluate : 0.685 Fit side-chains revert: symmetry clash REVERT: A 152 MET cc_start: 0.7790 (ptt) cc_final: 0.6471 (pmm) REVERT: A 216 ASN cc_start: 0.9155 (m110) cc_final: 0.8925 (p0) REVERT: A 224 TYR cc_start: 0.8506 (t80) cc_final: 0.8260 (t80) REVERT: A 302 LYS cc_start: 0.9331 (mmtp) cc_final: 0.9113 (mmtm) REVERT: B 315 ARG cc_start: 0.9260 (ttt90) cc_final: 0.8819 (ttm170) REVERT: B 321 PHE cc_start: 0.8565 (m-80) cc_final: 0.8294 (m-80) REVERT: B 367 ARG cc_start: 0.9287 (ptp90) cc_final: 0.9068 (ptt-90) REVERT: B 478 MET cc_start: 0.7549 (tpp) cc_final: 0.7281 (tpt) outliers start: 11 outliers final: 10 residues processed: 52 average time/residue: 0.1876 time to fit residues: 12.7827 Evaluate side-chains 55 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 45 time to evaluate : 0.578 ------------------------------------------------------------------------------- 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 265 LEU Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 362 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 64 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 15 optimal weight: 0.0670 chunk 47 optimal weight: 0.0970 chunk 7 optimal weight: 1.9990 overall best weight: 0.5516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 GLN B 176 GLN ** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2061 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= 0.167 Angle : 0.647 13.658 7189 Z= 0.308 Chirality : 0.042 0.248 804 Planarity : 0.003 0.031 928 Dihedral : 4.497 20.589 717 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % 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: -0.05 (0.33), residues: 646 helix: 2.20 (0.41), residues: 162 sheet: 0.12 (0.36), residues: 207 loop : -1.56 (0.35), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 443 HIS 0.005 0.001 HIS B 275 PHE 0.009 0.001 PHE B 321 TYR 0.012 0.001 TYR A 224 ARG 0.002 0.000 ARG A 349 ********************** 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 57 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 47 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.7707 (ptt) cc_final: 0.6414 (pmm) REVERT: A 224 TYR cc_start: 0.8465 (t80) cc_final: 0.7963 (t80) REVERT: A 302 LYS cc_start: 0.9309 (mmtp) cc_final: 0.9084 (mmtm) REVERT: B 315 ARG cc_start: 0.9259 (ttt90) cc_final: 0.8820 (ttm170) REVERT: B 478 MET cc_start: 0.7533 (tpp) cc_final: 0.7318 (tpt) outliers start: 10 outliers final: 9 residues processed: 54 average time/residue: 0.1872 time to fit residues: 13.4012 Evaluate side-chains 54 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 45 time to evaluate : 0.639 ------------------------------------------------------------------------------- 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 A residue 337 ASP Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 362 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 14 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 53 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 2 optimal weight: 0.1980 chunk 37 optimal weight: 6.9990 chunk 59 optimal weight: 0.0030 chunk 34 optimal weight: 0.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN ** 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 = 0.3291 r_free = 0.3291 target = 0.056538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.042532 restraints weight = 20142.676| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 4.59 r_work: 0.2756 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 5305 Z= 0.162 Angle : 0.628 13.872 7189 Z= 0.298 Chirality : 0.042 0.247 804 Planarity : 0.003 0.031 928 Dihedral : 4.486 20.329 717 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.78 % Allowed : 14.39 % Favored : 83.84 % 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: 2.13 (0.41), residues: 162 sheet: 0.06 (0.36), residues: 201 loop : -1.53 (0.34), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 443 HIS 0.005 0.001 HIS B 275 PHE 0.012 0.001 PHE A 227 TYR 0.016 0.001 TYR A 203 ARG 0.002 0.000 ARG A 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1482.38 seconds wall clock time: 27 minutes 35.22 seconds (1655.22 seconds total)