Starting phenix.real_space_refine on Wed Oct 9 22:00:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yoy_39460/10_2024/8yoy_39460.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yoy_39460/10_2024/8yoy_39460.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yoy_39460/10_2024/8yoy_39460.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yoy_39460/10_2024/8yoy_39460.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yoy_39460/10_2024/8yoy_39460.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yoy_39460/10_2024/8yoy_39460.cif" } resolution = 3.21 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= 0.018 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 47 5.16 5 C 3185 2.51 5 N 879 2.21 5 O 970 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 5081 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2248 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 14, 'TRANS': 274} Chain: "B" Number of atoms: 2833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2833 Classifications: {'peptide': 364} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 346} Time building chain proxies: 3.77, per 1000 atoms: 0.74 Number of scatterers: 5081 At special positions: 0 Unit cell: (63.99, 78.57, 136.89, 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 47 16.00 O 970 8.00 N 879 7.00 C 3185 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 352 " distance=2.03 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 423 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 605 " distance=2.03 Simple disulfide: pdb=" SG CYS A 466 " - pdb=" SG CYS A 546 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 495 " distance=2.03 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 567 " distance=2.03 Simple disulfide: pdb=" SG CYS A 485 " - pdb=" SG CYS A 516 " distance=2.03 Simple disulfide: pdb=" SG CYS A 504 " - pdb=" SG CYS A 518 " distance=2.03 Simple disulfide: pdb=" SG CYS A 520 " - pdb=" SG CYS A 533 " distance=2.02 Simple disulfide: pdb=" SG CYS A 556 " - pdb=" SG CYS A 569 " distance=2.03 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 241 " distance=2.03 Simple disulfide: pdb=" SG CYS B 244 " - pdb=" SG CYS B 365 " distance=2.03 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 297 " distance=2.03 Simple disulfide: pdb=" SG CYS B 410 " - pdb=" SG CYS B 426 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 465 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 957.6 milliseconds 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1212 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 10 sheets defined 15.0% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 328 through 334 removed outlier: 3.654A pdb=" N TRP A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 344 removed outlier: 3.915A pdb=" N TRP A 344 " --> pdb=" O PRO A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 363 Processing helix chain 'A' and resid 397 through 402 removed outlier: 3.877A pdb=" N GLN A 402 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 413 Processing helix chain 'A' and resid 442 through 448 removed outlier: 3.581A pdb=" N ARG A 446 " --> pdb=" O SER A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 552 through 556 removed outlier: 3.727A pdb=" N LYS A 555 " --> pdb=" O ASP A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 574 Processing helix chain 'B' and resid 142 through 147 Processing helix chain 'B' and resid 177 through 188 removed outlier: 3.786A pdb=" N GLY B 181 " --> pdb=" O ASN B 177 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA B 183 " --> pdb=" O ASN B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 298 removed outlier: 3.540A pdb=" N CYS B 297 " --> pdb=" O ALA B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 411 Processing helix chain 'B' and resid 480 through 491 removed outlier: 3.590A pdb=" N ALA B 490 " --> pdb=" O ARG B 486 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 337 through 338 Processing sheet with id=AA2, first strand: chain 'A' and resid 345 through 349 removed outlier: 3.584A pdb=" N GLU A 345 " --> pdb=" O LYS A 390 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS A 390 " --> pdb=" O GLU A 345 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER A 385 " --> pdb=" O ASN A 597 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER A 367 " --> pdb=" O TYR A 426 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N SER A 428 " --> pdb=" O THR A 365 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N THR A 365 " --> pdb=" O SER A 428 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 459 through 463 Processing sheet with id=AA4, first strand: chain 'A' and resid 466 through 468 removed outlier: 4.521A pdb=" N CYS A 466 " --> pdb=" O SER A 538 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS A 536 " --> pdb=" O SER A 468 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 504 through 507 Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 150 Processing sheet with id=AA7, first strand: chain 'B' and resid 196 through 200 Processing sheet with id=AA8, first strand: chain 'B' and resid 209 through 211 Processing sheet with id=AA9, first strand: chain 'B' and resid 270 through 275 removed outlier: 3.773A pdb=" N CYS B 281 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N VAL B 275 " --> pdb=" O HIS B 279 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N HIS B 279 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU B 348 " --> pdb=" O VAL B 331 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N VAL B 331 " --> pdb=" O LEU B 348 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N LYS B 350 " --> pdb=" O GLU B 329 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL B 328 " --> pdb=" O TRP B 308 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N TRP B 308 " --> pdb=" O VAL B 328 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 378 through 383 removed outlier: 4.246A pdb=" N CYS B 426 " --> pdb=" O ILE B 405 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N VAL B 473 " --> pdb=" O SER B 460 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR B 447 " --> pdb=" O TRP B 454 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU B 445 " --> pdb=" O ILE B 456 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER B 382 " --> pdb=" O PRO B 444 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N SER B 448 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N LEU B 378 " --> pdb=" O SER B 448 " (cutoff:3.500A) 125 hydrogen bonds defined for protein. 318 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: 1.37 Time building geometry restraints manager: 1.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1665 1.34 - 1.46: 1156 1.46 - 1.58: 2339 1.58 - 1.69: 0 1.69 - 1.81: 56 Bond restraints: 5216 Sorted by residual: bond pdb=" CA ASN A 351 " pdb=" CB ASN A 351 " ideal model delta sigma weight residual 1.530 1.543 -0.012 1.69e-02 3.50e+03 5.39e-01 bond pdb=" C PRO A 325 " pdb=" O PRO A 325 " ideal model delta sigma weight residual 1.235 1.227 0.008 1.30e-02 5.92e+03 4.08e-01 bond pdb=" CA PRO A 339 " pdb=" C PRO A 339 " ideal model delta sigma weight residual 1.526 1.519 0.007 1.13e-02 7.83e+03 3.40e-01 bond pdb=" CD1 TYR B 414 " pdb=" CE1 TYR B 414 " ideal model delta sigma weight residual 1.382 1.365 0.017 3.00e-02 1.11e+03 3.37e-01 bond pdb=" CB TYR B 414 " pdb=" CG TYR B 414 " ideal model delta sigma weight residual 1.512 1.500 0.012 2.20e-02 2.07e+03 3.14e-01 ... (remaining 5211 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 6855 1.12 - 2.24: 179 2.24 - 3.35: 46 3.35 - 4.47: 10 4.47 - 5.59: 4 Bond angle restraints: 7094 Sorted by residual: angle pdb=" C SER A 350 " pdb=" N ASN A 351 " pdb=" CA ASN A 351 " ideal model delta sigma weight residual 121.54 127.13 -5.59 1.91e+00 2.74e-01 8.56e+00 angle pdb=" C ALA B 468 " pdb=" N TYR B 469 " pdb=" CA TYR B 469 " ideal model delta sigma weight residual 121.54 126.84 -5.30 1.91e+00 2.74e-01 7.70e+00 angle pdb=" C GLY B 432 " pdb=" N ASN B 433 " pdb=" CA ASN B 433 " ideal model delta sigma weight residual 121.54 125.94 -4.40 1.91e+00 2.74e-01 5.30e+00 angle pdb=" C ASN A 585 " pdb=" N ASN A 586 " pdb=" CA ASN A 586 " ideal model delta sigma weight residual 121.54 125.24 -3.70 1.91e+00 2.74e-01 3.75e+00 angle pdb=" C ILE B 256 " pdb=" N VAL B 257 " pdb=" CA VAL B 257 " ideal model delta sigma weight residual 121.97 125.28 -3.31 1.80e+00 3.09e-01 3.38e+00 ... (remaining 7089 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.00: 2708 16.00 - 32.00: 314 32.00 - 47.99: 82 47.99 - 63.99: 13 63.99 - 79.99: 5 Dihedral angle restraints: 3122 sinusoidal: 1232 harmonic: 1890 Sorted by residual: dihedral pdb=" CB CYS A 474 " pdb=" SG CYS A 474 " pdb=" SG CYS A 495 " pdb=" CB CYS A 495 " ideal model delta sinusoidal sigma weight residual 93.00 166.04 -73.04 1 1.00e+01 1.00e-02 6.80e+01 dihedral pdb=" CB CYS B 133 " pdb=" SG CYS B 133 " pdb=" SG CYS B 148 " pdb=" CB CYS B 148 " ideal model delta sinusoidal sigma weight residual -86.00 -141.43 55.43 1 1.00e+01 1.00e-02 4.15e+01 dihedral pdb=" CB CYS A 520 " pdb=" SG CYS A 520 " pdb=" SG CYS A 533 " pdb=" CB CYS A 533 " ideal model delta sinusoidal sigma weight residual 93.00 134.92 -41.92 1 1.00e+01 1.00e-02 2.46e+01 ... (remaining 3119 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 443 0.029 - 0.059: 178 0.059 - 0.088: 88 0.088 - 0.118: 41 0.118 - 0.147: 5 Chirality restraints: 755 Sorted by residual: chirality pdb=" CA ASN A 351 " pdb=" N ASN A 351 " pdb=" C ASN A 351 " pdb=" CB ASN A 351 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.43e-01 chirality pdb=" CG LEU A 333 " pdb=" CB LEU A 333 " pdb=" CD1 LEU A 333 " pdb=" CD2 LEU A 333 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.58e-01 chirality pdb=" CA ILE B 291 " pdb=" N ILE B 291 " pdb=" C ILE B 291 " pdb=" CB ILE B 291 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.50e-01 ... (remaining 752 not shown) Planarity restraints: 923 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 421 " -0.029 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO B 422 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 422 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 422 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 287 " 0.023 5.00e-02 4.00e+02 3.45e-02 1.90e+00 pdb=" N PRO B 288 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 288 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 288 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 393 " -0.019 5.00e-02 4.00e+02 2.81e-02 1.27e+00 pdb=" N PRO A 394 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 394 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 394 " -0.016 5.00e-02 4.00e+02 ... (remaining 920 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 302 2.73 - 3.27: 5113 3.27 - 3.82: 8499 3.82 - 4.36: 10021 4.36 - 4.90: 16859 Nonbonded interactions: 40794 Sorted by model distance: nonbonded pdb=" O PRO A 496 " pdb=" OG1 THR A 499 " model vdw 2.189 3.040 nonbonded pdb=" OE1 GLU B 178 " pdb=" OG SER B 197 " model vdw 2.208 3.040 nonbonded pdb=" OG SER A 340 " pdb=" OD1 ASN A 343 " model vdw 2.221 3.040 nonbonded pdb=" OG SER A 562 " pdb=" OD1 ASN A 564 " model vdw 2.255 3.040 nonbonded pdb=" OE2 GLU B 299 " pdb=" OH TYR B 337 " model vdw 2.291 3.040 ... (remaining 40789 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=0.83 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.220 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.490 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4445 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 0.021 5216 Z= 0.227 Angle : 0.500 5.588 7094 Z= 0.270 Chirality : 0.043 0.147 755 Planarity : 0.004 0.045 923 Dihedral : 14.417 79.990 1859 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 16.00 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.32), residues: 649 helix: -2.36 (0.45), residues: 81 sheet: -0.27 (0.42), residues: 175 loop : -0.82 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 515 HIS 0.003 0.000 HIS B 296 PHE 0.005 0.001 PHE A 391 TYR 0.008 0.001 TYR B 222 ARG 0.003 0.000 ARG B 409 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.2009 time to fit residues: 37.5987 Evaluate side-chains 71 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.3980 chunk 37 optimal weight: 0.0070 chunk 58 optimal weight: 6.9990 overall best weight: 1.4804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4966 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5216 Z= 0.279 Angle : 0.674 8.795 7094 Z= 0.363 Chirality : 0.049 0.174 755 Planarity : 0.005 0.053 923 Dihedral : 4.731 18.919 704 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.78 % Allowed : 19.65 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.32), residues: 649 helix: -1.95 (0.52), residues: 77 sheet: -0.82 (0.40), residues: 175 loop : -0.59 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP B 168 HIS 0.009 0.002 HIS B 279 PHE 0.023 0.003 PHE B 311 TYR 0.010 0.002 TYR B 474 ARG 0.005 0.001 ARG B 409 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 83 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 LEU cc_start: 0.6069 (OUTLIER) cc_final: 0.5809 (pp) outliers start: 16 outliers final: 4 residues processed: 94 average time/residue: 0.2562 time to fit residues: 31.0729 Evaluate side-chains 61 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 56 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 479 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 32 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 48 optimal weight: 0.0370 chunk 39 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 overall best weight: 0.9262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 ASN ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 GLN ** B 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4999 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5216 Z= 0.211 Angle : 0.634 10.821 7094 Z= 0.331 Chirality : 0.048 0.236 755 Planarity : 0.005 0.055 923 Dihedral : 4.648 17.985 704 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 3.13 % Allowed : 20.00 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.32), residues: 649 helix: -1.32 (0.58), residues: 71 sheet: -0.91 (0.41), residues: 174 loop : -0.64 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP B 380 HIS 0.005 0.001 HIS A 512 PHE 0.028 0.002 PHE A 373 TYR 0.015 0.002 TYR A 465 ARG 0.014 0.001 ARG B 409 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 68 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 9 residues processed: 81 average time/residue: 0.2230 time to fit residues: 23.8477 Evaluate side-chains 69 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 60 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 410 CYS Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 479 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 57 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 27 optimal weight: 0.2980 chunk 39 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 535 GLN B 198 GLN ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5070 moved from start: 0.5073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5216 Z= 0.210 Angle : 0.619 7.539 7094 Z= 0.325 Chirality : 0.047 0.182 755 Planarity : 0.004 0.040 923 Dihedral : 4.684 20.540 704 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.55 % Favored : 94.30 % Rotamer: Outliers : 3.30 % Allowed : 21.57 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.32), residues: 649 helix: -1.60 (0.55), residues: 76 sheet: -0.98 (0.41), residues: 161 loop : -0.66 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 380 HIS 0.004 0.001 HIS B 274 PHE 0.016 0.002 PHE A 481 TYR 0.013 0.002 TYR A 427 ARG 0.008 0.001 ARG B 409 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 65 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 12 residues processed: 78 average time/residue: 0.1815 time to fit residues: 18.5156 Evaluate side-chains 70 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 58 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 362 LYS Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 410 CYS Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 479 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 35 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 46 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 15 optimal weight: 0.4980 chunk 20 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 198 GLN ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5233 moved from start: 0.5933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5216 Z= 0.242 Angle : 0.648 7.889 7094 Z= 0.346 Chirality : 0.048 0.172 755 Planarity : 0.004 0.042 923 Dihedral : 4.970 21.633 704 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 18.72 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.01 % Favored : 93.84 % Rotamer: Outliers : 3.48 % Allowed : 22.09 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.32), residues: 649 helix: -0.73 (0.66), residues: 58 sheet: -1.18 (0.38), residues: 179 loop : -0.64 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 454 HIS 0.004 0.001 HIS B 274 PHE 0.013 0.002 PHE B 311 TYR 0.012 0.002 TYR B 222 ARG 0.007 0.001 ARG B 409 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 72 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 537 LYS cc_start: 0.5537 (tptt) cc_final: 0.5273 (tptp) REVERT: B 403 LEU cc_start: 0.7426 (mt) cc_final: 0.7095 (mt) outliers start: 20 outliers final: 14 residues processed: 89 average time/residue: 0.1818 time to fit residues: 20.9175 Evaluate side-chains 75 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 61 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 587 ARG Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 198 GLN Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 410 CYS Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 479 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 36 optimal weight: 5.9990 chunk 15 optimal weight: 0.5980 chunk 61 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 5 optimal weight: 0.0010 chunk 20 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 35 optimal weight: 0.0570 overall best weight: 0.8706 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 GLN ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5180 moved from start: 0.6186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 5216 Z= 0.214 Angle : 0.670 8.658 7094 Z= 0.351 Chirality : 0.047 0.159 755 Planarity : 0.004 0.038 923 Dihedral : 4.905 20.800 704 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.24 % Favored : 94.61 % Rotamer: Outliers : 3.48 % Allowed : 23.48 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.32), residues: 649 helix: -0.46 (0.67), residues: 58 sheet: -1.10 (0.38), residues: 179 loop : -0.72 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 454 HIS 0.005 0.001 HIS B 274 PHE 0.028 0.002 PHE A 373 TYR 0.014 0.002 TYR B 414 ARG 0.005 0.001 ARG B 409 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 67 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 537 LYS cc_start: 0.5595 (tptt) cc_final: 0.5349 (tptp) outliers start: 20 outliers final: 17 residues processed: 83 average time/residue: 0.1821 time to fit residues: 19.6846 Evaluate side-chains 79 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 62 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 587 ARG Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 410 CYS Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 479 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 45 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 28 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5180 moved from start: 0.6430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5216 Z= 0.202 Angle : 0.661 7.752 7094 Z= 0.342 Chirality : 0.047 0.177 755 Planarity : 0.004 0.040 923 Dihedral : 4.783 19.443 704 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.16 % Favored : 93.68 % Rotamer: Outliers : 3.48 % Allowed : 24.17 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.32), residues: 649 helix: -0.51 (0.69), residues: 58 sheet: -1.09 (0.40), residues: 167 loop : -0.75 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 380 HIS 0.004 0.001 HIS B 274 PHE 0.017 0.002 PHE A 373 TYR 0.012 0.001 TYR B 222 ARG 0.004 0.001 ARG B 255 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 66 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 537 LYS cc_start: 0.5688 (tptt) cc_final: 0.5436 (tptp) outliers start: 20 outliers final: 17 residues processed: 82 average time/residue: 0.2369 time to fit residues: 25.2943 Evaluate side-chains 82 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 65 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 410 CYS Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 479 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 12 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 39 optimal weight: 0.3980 chunk 42 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 59 optimal weight: 0.0870 chunk 53 optimal weight: 0.8980 chunk 57 optimal weight: 8.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 159 GLN ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5126 moved from start: 0.6541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5216 Z= 0.183 Angle : 0.663 9.199 7094 Z= 0.340 Chirality : 0.047 0.172 755 Planarity : 0.004 0.036 923 Dihedral : 4.724 18.994 704 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.24 % Favored : 94.61 % Rotamer: Outliers : 3.13 % Allowed : 25.04 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.33), residues: 649 helix: -0.03 (0.74), residues: 52 sheet: -1.22 (0.38), residues: 183 loop : -0.55 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 380 HIS 0.004 0.001 HIS B 169 PHE 0.015 0.002 PHE B 319 TYR 0.015 0.001 TYR A 465 ARG 0.007 0.001 ARG A 464 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 64 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 537 LYS cc_start: 0.5738 (tptt) cc_final: 0.5495 (tptp) outliers start: 18 outliers final: 17 residues processed: 79 average time/residue: 0.1893 time to fit residues: 19.4439 Evaluate side-chains 77 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 60 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 587 ARG Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 410 CYS Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 479 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 59 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 51 optimal weight: 0.4980 chunk 54 optimal weight: 0.3980 chunk 57 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 28 optimal weight: 6.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5253 moved from start: 0.6922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5216 Z= 0.232 Angle : 0.676 8.606 7094 Z= 0.350 Chirality : 0.047 0.173 755 Planarity : 0.004 0.038 923 Dihedral : 4.929 21.952 704 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 19.93 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.16 % Favored : 93.68 % Rotamer: Outliers : 4.17 % Allowed : 23.83 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.32), residues: 649 helix: -0.61 (0.69), residues: 58 sheet: -1.28 (0.39), residues: 179 loop : -0.80 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 269 HIS 0.005 0.001 HIS B 169 PHE 0.014 0.002 PHE B 194 TYR 0.019 0.002 TYR A 465 ARG 0.004 0.001 ARG B 316 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 63 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 537 LYS cc_start: 0.5702 (tptt) cc_final: 0.5484 (tptp) outliers start: 24 outliers final: 20 residues processed: 81 average time/residue: 0.2537 time to fit residues: 25.8218 Evaluate side-chains 78 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 58 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 587 ARG Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 410 CYS Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 479 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 42 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 39 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 40 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 15 optimal weight: 0.3980 chunk 46 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5178 moved from start: 0.7003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5216 Z= 0.195 Angle : 0.705 9.287 7094 Z= 0.360 Chirality : 0.047 0.172 755 Planarity : 0.004 0.038 923 Dihedral : 4.833 25.115 704 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.08 % Favored : 94.76 % Rotamer: Outliers : 3.48 % Allowed : 24.52 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.33), residues: 649 helix: -0.53 (0.68), residues: 58 sheet: -1.34 (0.38), residues: 181 loop : -0.71 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 269 HIS 0.005 0.001 HIS B 169 PHE 0.012 0.002 PHE B 194 TYR 0.028 0.002 TYR A 465 ARG 0.004 0.001 ARG B 409 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 64 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 16 residues processed: 80 average time/residue: 0.1982 time to fit residues: 20.8277 Evaluate side-chains 76 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 60 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 587 ARG Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 410 CYS Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 479 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 7 optimal weight: 0.4980 chunk 14 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 HIS ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 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 = 0.4334 r_free = 0.4334 target = 0.096939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.081739 restraints weight = 21571.122| |-----------------------------------------------------------------------------| r_work (start): 0.4040 rms_B_bonded: 6.92 r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4040 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4040 r_free = 0.4040 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4041 r_free = 0.4041 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.4041 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.7185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5216 Z= 0.208 Angle : 0.714 8.587 7094 Z= 0.364 Chirality : 0.047 0.173 755 Planarity : 0.004 0.037 923 Dihedral : 4.850 24.129 704 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.24 % Favored : 94.61 % Rotamer: Outliers : 3.13 % Allowed : 25.04 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.33), residues: 649 helix: -0.52 (0.68), residues: 58 sheet: -1.45 (0.40), residues: 159 loop : -0.63 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 269 HIS 0.005 0.001 HIS B 169 PHE 0.011 0.001 PHE B 311 TYR 0.025 0.002 TYR A 465 ARG 0.004 0.001 ARG B 409 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1777.54 seconds wall clock time: 35 minutes 21.94 seconds (2121.94 seconds total)