Starting phenix.real_space_refine on Mon Sep 23 19:18:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lto_23517/09_2024/7lto_23517.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lto_23517/09_2024/7lto_23517.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lto_23517/09_2024/7lto_23517.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lto_23517/09_2024/7lto_23517.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lto_23517/09_2024/7lto_23517.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lto_23517/09_2024/7lto_23517.cif" } resolution = 3.2 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= 0.003 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 26 5.16 5 C 3114 2.51 5 N 776 2.21 5 O 838 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 4754 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2876 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 15, 'TRANS': 351} Chain breaks: 4 Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 181 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 97 Chain: "B" Number of atoms: 1878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1878 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 5, 'TRANS': 232} Chain breaks: 5 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 119 Time building chain proxies: 3.44, per 1000 atoms: 0.72 Number of scatterers: 4754 At special positions: 0 Unit cell: (64.904, 77.672, 101.08, 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 26 16.00 O 838 8.00 N 776 7.00 C 3114 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.12 Conformation dependent library (CDL) restraints added in 644.9 milliseconds 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1184 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 0 sheets defined 58.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 25 through 41 removed outlier: 3.660A pdb=" N LEU A 30 " --> pdb=" O GLU A 26 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA A 31 " --> pdb=" O LYS A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 53 removed outlier: 3.793A pdb=" N LEU A 51 " --> pdb=" O VAL A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 76 removed outlier: 3.971A pdb=" N VAL A 71 " --> pdb=" O ASP A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 91 removed outlier: 4.030A pdb=" N LEU A 87 " --> pdb=" O LYS A 83 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 116 Processing helix chain 'A' and resid 126 through 140 removed outlier: 3.775A pdb=" N ALA A 138 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP A 140 " --> pdb=" O PHE A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 220 Processing helix chain 'A' and resid 229 through 239 Processing helix chain 'A' and resid 239 through 255 removed outlier: 3.920A pdb=" N CYS A 253 " --> pdb=" O ASP A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 260 removed outlier: 3.985A pdb=" N GLN A 260 " --> pdb=" O ASP A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 302 removed outlier: 3.714A pdb=" N PHE A 297 " --> pdb=" O PHE A 293 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER A 298 " --> pdb=" O ALA A 294 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE A 302 " --> pdb=" O SER A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 363 removed outlier: 4.329A pdb=" N LEU A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A 362 " --> pdb=" O CYS A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 391 Processing helix chain 'A' and resid 394 through 403 removed outlier: 3.936A pdb=" N PHE A 402 " --> pdb=" O PHE A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 430 removed outlier: 3.550A pdb=" N GLU A 424 " --> pdb=" O GLY A 420 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU A 426 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LYS A 427 " --> pdb=" O SER A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 511 removed outlier: 3.569A pdb=" N ASP A 504 " --> pdb=" O GLU A 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 217 Processing helix chain 'B' and resid 219 through 225 Processing helix chain 'B' and resid 245 through 253 Processing helix chain 'B' and resid 283 through 292 removed outlier: 3.513A pdb=" N MET B 292 " --> pdb=" O LEU B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 317 removed outlier: 3.541A pdb=" N ARG B 304 " --> pdb=" O ASN B 300 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE B 306 " --> pdb=" O ASP B 302 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP B 317 " --> pdb=" O CYS B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 322 Processing helix chain 'B' and resid 329 through 336 Processing helix chain 'B' and resid 339 through 346 Processing helix chain 'B' and resid 354 through 366 removed outlier: 4.065A pdb=" N LEU B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG B 361 " --> pdb=" O PHE B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 378 removed outlier: 3.663A pdb=" N ARG B 375 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ARG B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 397 Processing helix chain 'B' and resid 404 through 416 Processing helix chain 'B' and resid 432 through 441 removed outlier: 3.753A pdb=" N CYS B 436 " --> pdb=" O TYR B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 462 removed outlier: 4.018A pdb=" N LEU B 453 " --> pdb=" O GLU B 449 " (cutoff:3.500A) 203 hydrogen bonds defined for protein. 609 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: 1.08 Time building geometry restraints manager: 1.32 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: 1470 1.34 - 1.46: 861 1.46 - 1.58: 2484 1.58 - 1.70: 0 1.70 - 1.82: 38 Bond restraints: 4853 Sorted by residual: bond pdb=" CA GLU A 193 " pdb=" C GLU A 193 " ideal model delta sigma weight residual 1.524 1.556 -0.032 1.24e-02 6.50e+03 6.64e+00 bond pdb=" CA LEU A 192 " pdb=" C LEU A 192 " ideal model delta sigma weight residual 1.522 1.545 -0.023 1.25e-02 6.40e+03 3.33e+00 bond pdb=" CA ALA B 323 " pdb=" C ALA B 323 " ideal model delta sigma weight residual 1.530 1.511 0.020 1.23e-02 6.61e+03 2.58e+00 bond pdb=" C MET A 241 " pdb=" O MET A 241 " ideal model delta sigma weight residual 1.244 1.228 0.016 1.00e-02 1.00e+04 2.43e+00 bond pdb=" C TRP A 240 " pdb=" O TRP A 240 " ideal model delta sigma weight residual 1.236 1.219 0.018 1.29e-02 6.01e+03 1.85e+00 ... (remaining 4848 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 6247 1.45 - 2.89: 247 2.89 - 4.34: 49 4.34 - 5.78: 13 5.78 - 7.23: 7 Bond angle restraints: 6563 Sorted by residual: angle pdb=" N GLN A 194 " pdb=" CA GLN A 194 " pdb=" C GLN A 194 " ideal model delta sigma weight residual 112.57 119.12 -6.55 1.13e+00 7.83e-01 3.36e+01 angle pdb=" N TRP A 240 " pdb=" CA TRP A 240 " pdb=" C TRP A 240 " ideal model delta sigma weight residual 112.23 119.19 -6.96 1.26e+00 6.30e-01 3.06e+01 angle pdb=" C ASP A 91 " pdb=" N PRO A 92 " pdb=" CA PRO A 92 " ideal model delta sigma weight residual 119.24 124.34 -5.10 1.04e+00 9.25e-01 2.40e+01 angle pdb=" N LEU A 192 " pdb=" CA LEU A 192 " pdb=" C LEU A 192 " ideal model delta sigma weight residual 114.09 106.86 7.23 1.55e+00 4.16e-01 2.17e+01 angle pdb=" N LEU A 131 " pdb=" CA LEU A 131 " pdb=" C LEU A 131 " ideal model delta sigma weight residual 112.04 105.82 6.22 1.44e+00 4.82e-01 1.86e+01 ... (remaining 6558 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 2596 17.82 - 35.64: 241 35.64 - 53.46: 58 53.46 - 71.28: 10 71.28 - 89.11: 5 Dihedral angle restraints: 2910 sinusoidal: 1106 harmonic: 1804 Sorted by residual: dihedral pdb=" CA GLU B 398 " pdb=" C GLU B 398 " pdb=" N PHE B 399 " pdb=" CA PHE B 399 " ideal model delta harmonic sigma weight residual 180.00 162.12 17.88 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA SER A 411 " pdb=" C SER A 411 " pdb=" N TYR A 412 " pdb=" CA TYR A 412 " ideal model delta harmonic sigma weight residual 180.00 162.21 17.79 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA ASN B 345 " pdb=" C ASN B 345 " pdb=" N SER B 346 " pdb=" CA SER B 346 " ideal model delta harmonic sigma weight residual 180.00 163.22 16.78 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 2907 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 695 0.075 - 0.150: 54 0.150 - 0.225: 7 0.225 - 0.299: 3 0.299 - 0.374: 1 Chirality restraints: 760 Sorted by residual: chirality pdb=" CA TRP A 240 " pdb=" N TRP A 240 " pdb=" C TRP A 240 " pdb=" CB TRP A 240 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.50e+00 chirality pdb=" CA TYR A 81 " pdb=" N TYR A 81 " pdb=" C TYR A 81 " pdb=" CB TYR A 81 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA TYR A 82 " pdb=" N TYR A 82 " pdb=" C TYR A 82 " pdb=" CB TYR A 82 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 757 not shown) Planarity restraints: 819 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 193 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.28e+00 pdb=" C GLU A 193 " -0.031 2.00e-02 2.50e+03 pdb=" O GLU A 193 " 0.012 2.00e-02 2.50e+03 pdb=" N GLN A 194 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 411 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C SER A 411 " 0.029 2.00e-02 2.50e+03 pdb=" O SER A 411 " -0.011 2.00e-02 2.50e+03 pdb=" N TYR A 412 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 239 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.62e+00 pdb=" C ILE A 239 " 0.028 2.00e-02 2.50e+03 pdb=" O ILE A 239 " -0.011 2.00e-02 2.50e+03 pdb=" N TRP A 240 " -0.009 2.00e-02 2.50e+03 ... (remaining 816 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 929 2.77 - 3.30: 4572 3.30 - 3.83: 7256 3.83 - 4.37: 9095 4.37 - 4.90: 15381 Nonbonded interactions: 37233 Sorted by model distance: nonbonded pdb=" O PHE A 50 " pdb=" NE2 GLN A 54 " model vdw 2.232 3.120 nonbonded pdb=" O ARG A 387 " pdb=" OG SER A 391 " model vdw 2.281 3.040 nonbonded pdb=" O LYS A 343 " pdb=" OG SER A 347 " model vdw 2.282 3.040 nonbonded pdb=" NZ LYS A 207 " pdb=" O VAL A 321 " model vdw 2.311 3.120 nonbonded pdb=" NE2 GLN B 370 " pdb=" O THR B 414 " model vdw 2.311 3.120 ... (remaining 37228 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.010 Find NCS groups from input model: 0.040 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 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 0.032 4853 Z= 0.219 Angle : 0.707 7.229 6563 Z= 0.447 Chirality : 0.049 0.374 760 Planarity : 0.003 0.037 819 Dihedral : 15.408 89.105 1726 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 3.25 % Allowed : 15.45 % Favored : 81.30 % 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: -4.26 (0.29), residues: 583 helix: -2.13 (0.25), residues: 333 sheet: None (None), residues: 0 loop : -3.81 (0.31), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 200 HIS 0.002 0.000 HIS A 46 PHE 0.011 0.001 PHE A 413 TYR 0.009 0.001 TYR A 82 ARG 0.001 0.000 ARG A 387 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 0.716 Fit side-chains revert: symmetry clash REVERT: A 337 LYS cc_start: 0.8674 (mttm) cc_final: 0.8441 (mmmt) outliers start: 16 outliers final: 11 residues processed: 111 average time/residue: 0.1850 time to fit residues: 25.7419 Evaluate side-chains 88 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 77 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLN Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 416 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 0.0470 chunk 44 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 17 optimal weight: 0.2980 chunk 28 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 HIS A 90 ASN A 94 ASN A 134 GLN A 345 GLN A 383 GLN B 201 HIS B 206 ASN B 211 GLN B 277 ASN ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 364 GLN B 389 GLN B 407 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4853 Z= 0.176 Angle : 0.565 6.907 6563 Z= 0.289 Chirality : 0.040 0.145 760 Planarity : 0.004 0.039 819 Dihedral : 6.402 51.118 660 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 3.05 % Allowed : 16.87 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.32), residues: 583 helix: -0.71 (0.28), residues: 343 sheet: None (None), residues: 0 loop : -3.42 (0.32), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 240 HIS 0.003 0.001 HIS A 46 PHE 0.012 0.001 PHE B 348 TYR 0.021 0.001 TYR B 432 ARG 0.002 0.000 ARG A 387 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 90 time to evaluate : 0.519 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 11 residues processed: 100 average time/residue: 0.1393 time to fit residues: 18.4896 Evaluate side-chains 98 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 87 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLN Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 416 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 29 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 53 optimal weight: 0.4980 chunk 57 optimal weight: 0.2980 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN B 339 ASN B 389 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4853 Z= 0.195 Angle : 0.557 7.009 6563 Z= 0.281 Chirality : 0.040 0.131 760 Planarity : 0.003 0.043 819 Dihedral : 6.197 49.934 656 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 3.66 % Allowed : 18.09 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.34), residues: 583 helix: -0.04 (0.29), residues: 348 sheet: None (None), residues: 0 loop : -3.15 (0.34), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 240 HIS 0.001 0.000 HIS B 359 PHE 0.015 0.001 PHE B 396 TYR 0.009 0.001 TYR B 209 ARG 0.002 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 93 time to evaluate : 0.569 Fit side-chains REVERT: B 369 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8407 (pp) REVERT: B 450 ILE cc_start: 0.6899 (mp) cc_final: 0.6401 (mp) outliers start: 18 outliers final: 11 residues processed: 104 average time/residue: 0.1486 time to fit residues: 20.7974 Evaluate side-chains 100 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 88 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 416 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 27 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 28 optimal weight: 0.4980 chunk 51 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN A 508 GLN B 389 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4853 Z= 0.208 Angle : 0.572 7.168 6563 Z= 0.286 Chirality : 0.040 0.125 760 Planarity : 0.003 0.044 819 Dihedral : 5.798 50.359 650 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 3.66 % Allowed : 19.11 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.34), residues: 583 helix: 0.24 (0.29), residues: 343 sheet: None (None), residues: 0 loop : -2.98 (0.34), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 200 HIS 0.001 0.000 HIS B 359 PHE 0.014 0.001 PHE B 348 TYR 0.019 0.001 TYR B 432 ARG 0.001 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 89 time to evaluate : 0.617 Fit side-chains revert: symmetry clash REVERT: B 369 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8364 (pp) REVERT: B 450 ILE cc_start: 0.6930 (mp) cc_final: 0.6410 (mp) outliers start: 18 outliers final: 14 residues processed: 100 average time/residue: 0.1448 time to fit residues: 19.4250 Evaluate side-chains 95 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 80 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 416 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 0 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 23 optimal weight: 0.0010 chunk 48 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 51 optimal weight: 0.0980 chunk 14 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN B 389 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4853 Z= 0.172 Angle : 0.554 9.265 6563 Z= 0.276 Chirality : 0.039 0.122 760 Planarity : 0.003 0.045 819 Dihedral : 5.625 49.850 650 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 3.25 % Allowed : 20.33 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.35), residues: 583 helix: 0.47 (0.29), residues: 343 sheet: None (None), residues: 0 loop : -2.82 (0.34), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 200 HIS 0.001 0.000 HIS B 342 PHE 0.011 0.001 PHE B 307 TYR 0.013 0.001 TYR B 209 ARG 0.001 0.000 ARG A 132 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 93 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 CYS cc_start: 0.8001 (p) cc_final: 0.7650 (p) REVERT: B 369 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8384 (pp) REVERT: B 450 ILE cc_start: 0.7002 (mp) cc_final: 0.6491 (mp) outliers start: 16 outliers final: 11 residues processed: 104 average time/residue: 0.1386 time to fit residues: 19.2726 Evaluate side-chains 98 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 86 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 416 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 14 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 29 optimal weight: 0.0070 chunk 55 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 41 optimal weight: 0.0570 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN B 277 ASN B 389 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4853 Z= 0.157 Angle : 0.574 16.017 6563 Z= 0.279 Chirality : 0.039 0.120 760 Planarity : 0.003 0.046 819 Dihedral : 5.384 49.321 649 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.46 % Allowed : 21.54 % Favored : 75.00 % 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: -0.93 (0.35), residues: 583 helix: 0.67 (0.29), residues: 347 sheet: None (None), residues: 0 loop : -2.70 (0.35), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 200 HIS 0.001 0.000 HIS B 359 PHE 0.012 0.001 PHE B 396 TYR 0.020 0.001 TYR B 432 ARG 0.001 0.000 ARG A 387 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 91 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 CYS cc_start: 0.7993 (p) cc_final: 0.7601 (p) REVERT: B 369 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8365 (pp) REVERT: B 450 ILE cc_start: 0.7012 (mp) cc_final: 0.6462 (mp) outliers start: 17 outliers final: 11 residues processed: 103 average time/residue: 0.1393 time to fit residues: 19.1737 Evaluate side-chains 97 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 85 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 369 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 32 optimal weight: 1.9990 chunk 48 optimal weight: 0.0170 chunk 31 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 22 optimal weight: 0.1980 chunk 33 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.5820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN B 277 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4853 Z= 0.181 Angle : 0.585 14.578 6563 Z= 0.284 Chirality : 0.039 0.121 760 Planarity : 0.003 0.046 819 Dihedral : 4.696 53.092 645 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 4.47 % Allowed : 20.93 % Favored : 74.59 % 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: -0.82 (0.35), residues: 583 helix: 0.75 (0.30), residues: 346 sheet: None (None), residues: 0 loop : -2.63 (0.35), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 200 HIS 0.001 0.000 HIS B 368 PHE 0.012 0.001 PHE A 55 TYR 0.011 0.001 TYR B 209 ARG 0.001 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 91 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 CYS cc_start: 0.8030 (p) cc_final: 0.7643 (p) REVERT: A 424 GLU cc_start: 0.6799 (OUTLIER) cc_final: 0.6533 (mt-10) REVERT: B 369 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8395 (pp) REVERT: B 450 ILE cc_start: 0.7017 (mp) cc_final: 0.6480 (mp) outliers start: 22 outliers final: 16 residues processed: 107 average time/residue: 0.1379 time to fit residues: 19.9312 Evaluate side-chains 104 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 86 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 416 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 28 optimal weight: 0.2980 chunk 5 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN B 277 ASN B 354 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4853 Z= 0.240 Angle : 0.628 14.359 6563 Z= 0.305 Chirality : 0.041 0.128 760 Planarity : 0.003 0.044 819 Dihedral : 4.900 55.168 645 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 4.67 % Allowed : 21.14 % Favored : 74.19 % 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: -0.94 (0.35), residues: 583 helix: 0.64 (0.29), residues: 346 sheet: None (None), residues: 0 loop : -2.65 (0.35), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 240 HIS 0.002 0.000 HIS B 342 PHE 0.017 0.002 PHE B 348 TYR 0.020 0.001 TYR B 432 ARG 0.002 0.000 ARG A 387 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 84 time to evaluate : 0.578 Fit side-chains revert: symmetry clash REVERT: A 53 CYS cc_start: 0.8130 (p) cc_final: 0.7699 (p) REVERT: A 424 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.6590 (mt-10) REVERT: B 336 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7136 (mt-10) REVERT: B 369 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8396 (pp) REVERT: B 450 ILE cc_start: 0.7052 (OUTLIER) cc_final: 0.6532 (mp) outliers start: 23 outliers final: 15 residues processed: 99 average time/residue: 0.1444 time to fit residues: 18.9552 Evaluate side-chains 98 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 79 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain B residue 450 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 23 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 16 optimal weight: 0.2980 chunk 47 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 52 optimal weight: 0.3980 chunk 34 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 58 optimal weight: 0.0070 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN B 277 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4853 Z= 0.173 Angle : 0.601 13.683 6563 Z= 0.293 Chirality : 0.039 0.131 760 Planarity : 0.003 0.045 819 Dihedral : 4.695 53.643 645 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 4.07 % Allowed : 22.36 % Favored : 73.58 % 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: -0.67 (0.35), residues: 583 helix: 0.85 (0.30), residues: 348 sheet: None (None), residues: 0 loop : -2.56 (0.36), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 200 HIS 0.001 0.000 HIS B 342 PHE 0.011 0.001 PHE A 55 TYR 0.011 0.001 TYR B 209 ARG 0.002 0.000 ARG A 387 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 89 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 CYS cc_start: 0.8057 (p) cc_final: 0.7624 (p) REVERT: A 424 GLU cc_start: 0.6876 (OUTLIER) cc_final: 0.6559 (mt-10) REVERT: B 292 MET cc_start: 0.7054 (ttp) cc_final: 0.6815 (ttt) REVERT: B 369 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8388 (pp) REVERT: B 450 ILE cc_start: 0.7077 (OUTLIER) cc_final: 0.6542 (mp) outliers start: 20 outliers final: 16 residues processed: 102 average time/residue: 0.1471 time to fit residues: 19.9634 Evaluate side-chains 104 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 85 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain B residue 450 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 6 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN B 277 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4853 Z= 0.208 Angle : 0.636 13.600 6563 Z= 0.309 Chirality : 0.041 0.184 760 Planarity : 0.003 0.045 819 Dihedral : 4.777 54.712 645 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 3.86 % Allowed : 22.56 % Favored : 73.58 % 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: -0.68 (0.35), residues: 583 helix: 0.85 (0.29), residues: 346 sheet: None (None), residues: 0 loop : -2.54 (0.36), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 200 HIS 0.001 0.000 HIS B 342 PHE 0.014 0.001 PHE B 348 TYR 0.020 0.001 TYR B 432 ARG 0.002 0.000 ARG A 387 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 86 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 CYS cc_start: 0.8101 (p) cc_final: 0.7695 (p) REVERT: A 424 GLU cc_start: 0.6872 (OUTLIER) cc_final: 0.6557 (mt-10) REVERT: B 369 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8382 (pp) REVERT: B 450 ILE cc_start: 0.7102 (OUTLIER) cc_final: 0.6559 (mp) outliers start: 19 outliers final: 15 residues processed: 97 average time/residue: 0.1384 time to fit residues: 17.9628 Evaluate side-chains 101 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 83 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain B residue 450 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 46 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 53 optimal weight: 0.2980 chunk 31 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN B 277 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.176016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.158990 restraints weight = 6099.883| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 1.58 r_work: 0.3863 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3734 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4853 Z= 0.199 Angle : 0.636 13.391 6563 Z= 0.308 Chirality : 0.041 0.183 760 Planarity : 0.003 0.045 819 Dihedral : 4.772 55.144 645 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 4.07 % Allowed : 22.36 % Favored : 73.58 % 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: -0.61 (0.35), residues: 583 helix: 0.92 (0.29), residues: 346 sheet: None (None), residues: 0 loop : -2.53 (0.36), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 200 HIS 0.001 0.000 HIS B 342 PHE 0.013 0.001 PHE B 348 TYR 0.012 0.001 TYR B 209 ARG 0.002 0.000 ARG A 387 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1411.56 seconds wall clock time: 25 minutes 43.47 seconds (1543.47 seconds total)