Starting phenix.real_space_refine on Sun Mar 10 16:25:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yd1_33745/03_2024/7yd1_33745.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yd1_33745/03_2024/7yd1_33745.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yd1_33745/03_2024/7yd1_33745.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yd1_33745/03_2024/7yd1_33745.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yd1_33745/03_2024/7yd1_33745.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yd1_33745/03_2024/7yd1_33745.pdb" } resolution = 2.99 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= 0.011 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 16 5.16 5 C 2104 2.51 5 N 550 2.21 5 O 635 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 346": "NH1" <-> "NH2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "C ARG 454": "NH1" <-> "NH2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "A ARG 60": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3305 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1588 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 185} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 931 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 7, 'TRANS': 114} Chain: "B" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 786 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Time building chain proxies: 2.26, per 1000 atoms: 0.68 Number of scatterers: 3305 At special positions: 0 Unit cell: (84.056, 84.056, 92.568, 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 16 16.00 O 635 8.00 N 550 7.00 C 2104 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 90 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 636.8 milliseconds 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 792 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 9 sheets defined 6.8% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 370 Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'B' and resid 81 through 85 removed outlier: 3.523A pdb=" N ASP B 84 " --> pdb=" O GLN B 81 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLU B 85 " --> pdb=" O ALA B 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 81 through 85' Processing sheet with id=AA1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.532A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.542A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.508A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 3 through 6 Processing sheet with id=AA5, first strand: chain 'A' and resid 11 through 12 Processing sheet with id=AA6, first strand: chain 'A' and resid 37 through 40 removed outlier: 6.657A pdb=" N TRP A 38 " --> pdb=" O LEU A 50 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 9 through 12 Processing sheet with id=AA8, first strand: chain 'B' and resid 18 through 23 Processing sheet with id=AA9, first strand: chain 'B' and resid 47 through 50 removed outlier: 6.771A pdb=" N TRP B 37 " --> pdb=" O MET B 49 " (cutoff:3.500A) 77 hydrogen bonds defined for protein. 177 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: 0.79 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1045 1.34 - 1.46: 849 1.46 - 1.58: 1476 1.58 - 1.69: 0 1.69 - 1.81: 19 Bond restraints: 3389 Sorted by residual: bond pdb=" N ASP B 52 " pdb=" CA ASP B 52 " ideal model delta sigma weight residual 1.457 1.467 -0.010 1.32e-02 5.74e+03 5.68e-01 bond pdb=" C SER A 67 " pdb=" N SER A 68 " ideal model delta sigma weight residual 1.332 1.323 0.009 1.40e-02 5.10e+03 4.49e-01 bond pdb=" CA PHE A 107 " pdb=" C PHE A 107 " ideal model delta sigma weight residual 1.531 1.524 0.007 1.08e-02 8.57e+03 4.23e-01 bond pdb=" CG PRO A 89 " pdb=" CD PRO A 89 " ideal model delta sigma weight residual 1.503 1.486 0.017 3.40e-02 8.65e+02 2.47e-01 bond pdb=" C TYR B 51 " pdb=" N ASP B 52 " ideal model delta sigma weight residual 1.332 1.339 -0.006 1.37e-02 5.33e+03 2.17e-01 ... (remaining 3384 not shown) Histogram of bond angle deviations from ideal: 100.84 - 107.47: 135 107.47 - 114.09: 1861 114.09 - 120.72: 1291 120.72 - 127.35: 1295 127.35 - 133.98: 37 Bond angle restraints: 4619 Sorted by residual: angle pdb=" N VAL B 53 " pdb=" CA VAL B 53 " pdb=" C VAL B 53 " ideal model delta sigma weight residual 109.34 113.82 -4.48 2.08e+00 2.31e-01 4.63e+00 angle pdb=" CA TYR B 51 " pdb=" CB TYR B 51 " pdb=" CG TYR B 51 " ideal model delta sigma weight residual 113.90 117.74 -3.84 1.80e+00 3.09e-01 4.56e+00 angle pdb=" C ASP B 52 " pdb=" N VAL B 53 " pdb=" CA VAL B 53 " ideal model delta sigma weight residual 121.97 125.50 -3.53 1.80e+00 3.09e-01 3.85e+00 angle pdb=" CA PHE A 107 " pdb=" C PHE A 107 " pdb=" N ASP A 108 " ideal model delta sigma weight residual 114.17 117.17 -3.00 1.55e+00 4.16e-01 3.75e+00 angle pdb=" C TYR B 51 " pdb=" N ASP B 52 " pdb=" CA ASP B 52 " ideal model delta sigma weight residual 121.31 124.15 -2.84 1.49e+00 4.50e-01 3.63e+00 ... (remaining 4614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.48: 1791 9.48 - 18.96: 128 18.96 - 28.44: 62 28.44 - 37.93: 24 37.93 - 47.41: 4 Dihedral angle restraints: 2009 sinusoidal: 766 harmonic: 1243 Sorted by residual: dihedral pdb=" CA ASP B 52 " pdb=" C ASP B 52 " pdb=" N VAL B 53 " pdb=" CA VAL B 53 " ideal model delta harmonic sigma weight residual -180.00 -156.24 -23.76 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA TYR B 51 " pdb=" C TYR B 51 " pdb=" N ASP B 52 " pdb=" CA ASP B 52 " ideal model delta harmonic sigma weight residual -180.00 -161.50 -18.50 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA SER B 26 " pdb=" C SER B 26 " pdb=" N SER B 27 " pdb=" CA SER B 27 " ideal model delta harmonic sigma weight residual -180.00 -162.42 -17.58 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 2006 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 279 0.024 - 0.048: 143 0.048 - 0.072: 48 0.072 - 0.096: 26 0.096 - 0.120: 20 Chirality restraints: 516 Sorted by residual: chirality pdb=" CA ILE B 20 " pdb=" N ILE B 20 " pdb=" C ILE B 20 " pdb=" CB ILE B 20 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.59e-01 chirality pdb=" CA VAL B 98 " pdb=" N VAL B 98 " pdb=" C VAL B 98 " pdb=" CB VAL B 98 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.59e-01 chirality pdb=" CA ILE B 77 " pdb=" N ILE B 77 " pdb=" C ILE B 77 " pdb=" CB ILE B 77 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.49e-01 ... (remaining 513 not shown) Planarity restraints: 590 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 462 " 0.034 5.00e-02 4.00e+02 5.16e-02 4.26e+00 pdb=" N PRO C 463 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 463 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 463 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 88 " -0.023 5.00e-02 4.00e+02 3.47e-02 1.92e+00 pdb=" N PRO A 89 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 89 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 89 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 383 " 0.019 5.00e-02 4.00e+02 2.88e-02 1.33e+00 pdb=" N PRO C 384 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO C 384 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 384 " 0.016 5.00e-02 4.00e+02 ... (remaining 587 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 319 2.75 - 3.29: 3186 3.29 - 3.83: 5375 3.83 - 4.36: 6403 4.36 - 4.90: 11033 Nonbonded interactions: 26316 Sorted by model distance: nonbonded pdb=" OG SER A 7 " pdb=" OG1 THR A 21 " model vdw 2.215 2.440 nonbonded pdb=" OG1 THR B 5 " pdb=" OG1 THR B 23 " model vdw 2.276 2.440 nonbonded pdb=" OG1 THR A 70 " pdb=" OG1 THR A 83 " model vdw 2.289 2.440 nonbonded pdb=" O ILE A 106 " pdb=" OH TYR B 38 " model vdw 2.308 2.440 nonbonded pdb=" O THR C 393 " pdb=" OG1 THR C 523 " model vdw 2.310 2.440 ... (remaining 26311 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 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: 6.480 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.960 Find NCS groups from input model: 0.100 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:11.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 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 : 0.002 0.017 3389 Z= 0.104 Angle : 0.491 9.075 4619 Z= 0.261 Chirality : 0.039 0.120 516 Planarity : 0.004 0.052 590 Dihedral : 8.999 47.407 1199 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.95 % Favored : 90.05 % Rotamer: Outliers : 5.46 % Allowed : 5.19 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.06 (0.37), residues: 422 helix: -5.17 (0.22), residues: 20 sheet: -1.77 (0.41), residues: 144 loop : -3.20 (0.35), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 HIS 0.000 0.000 HIS B 41 PHE 0.007 0.001 PHE C 429 TYR 0.018 0.001 TYR B 51 ARG 0.002 0.000 ARG C 457 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 109 time to evaluate : 0.408 Fit side-chains REVERT: C 346 ARG cc_start: 0.6893 (tpt90) cc_final: 0.6617 (tpt90) REVERT: C 392 PHE cc_start: 0.8236 (m-80) cc_final: 0.8025 (m-80) REVERT: C 395 VAL cc_start: 0.8815 (OUTLIER) cc_final: 0.8421 (m) REVERT: C 399 SER cc_start: 0.8317 (m) cc_final: 0.7941 (p) REVERT: C 429 PHE cc_start: 0.7342 (t80) cc_final: 0.7096 (t80) REVERT: C 437 ASN cc_start: 0.7918 (t0) cc_final: 0.7672 (t0) REVERT: C 438 SER cc_start: 0.8450 (p) cc_final: 0.8188 (p) REVERT: C 455 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7534 (tm) REVERT: C 456 PHE cc_start: 0.6700 (m-80) cc_final: 0.6210 (m-80) REVERT: C 494 SER cc_start: 0.8374 (t) cc_final: 0.8150 (p) REVERT: C 515 PHE cc_start: 0.8611 (m-10) cc_final: 0.8263 (m-10) REVERT: A 18 LEU cc_start: 0.8044 (mt) cc_final: 0.7368 (mp) REVERT: A 47 LEU cc_start: 0.8403 (mt) cc_final: 0.8120 (mt) REVERT: A 52 LEU cc_start: 0.8743 (tp) cc_final: 0.8466 (tp) REVERT: A 61 TYR cc_start: 0.8444 (m-80) cc_final: 0.7757 (m-80) REVERT: A 87 MET cc_start: 0.6147 (mmm) cc_final: 0.5527 (mmm) REVERT: A 107 PHE cc_start: 0.8136 (m-10) cc_final: 0.7886 (m-10) REVERT: A 112 GLN cc_start: 0.6423 (pp30) cc_final: 0.6127 (pp30) outliers start: 20 outliers final: 5 residues processed: 124 average time/residue: 0.4836 time to fit residues: 63.8302 Evaluate side-chains 107 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 100 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain A residue 92 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.0980 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 chunk 32 optimal weight: 0.7980 chunk 12 optimal weight: 0.1980 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 0.0980 chunk 37 optimal weight: 0.6980 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 409 GLN C 439 ASN C 460 ASN C 506 GLN A 16 GLN A 78 ASN A 79 GLN B 39 GLN B 62 ASN B 81 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3389 Z= 0.220 Angle : 0.580 10.738 4619 Z= 0.287 Chirality : 0.043 0.216 516 Planarity : 0.005 0.054 590 Dihedral : 5.479 44.021 479 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer: Outliers : 4.37 % Allowed : 13.39 % Favored : 82.24 % 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: -3.44 (0.38), residues: 422 helix: -5.05 (0.26), residues: 20 sheet: -1.32 (0.42), residues: 144 loop : -2.76 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 49 HIS 0.001 0.000 HIS B 41 PHE 0.012 0.001 PHE A 24 TYR 0.017 0.001 TYR B 51 ARG 0.002 0.000 ARG C 457 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 0.392 Fit side-chains REVERT: C 346 ARG cc_start: 0.6942 (tpt90) cc_final: 0.6603 (tpt90) REVERT: C 392 PHE cc_start: 0.8293 (m-80) cc_final: 0.7858 (m-80) REVERT: C 395 VAL cc_start: 0.8799 (OUTLIER) cc_final: 0.8382 (m) REVERT: C 399 SER cc_start: 0.8403 (m) cc_final: 0.8099 (p) REVERT: C 407 VAL cc_start: 0.8670 (t) cc_final: 0.8454 (p) REVERT: C 429 PHE cc_start: 0.7498 (t80) cc_final: 0.7200 (t80) REVERT: C 438 SER cc_start: 0.8518 (p) cc_final: 0.8227 (p) REVERT: C 473 TYR cc_start: 0.6692 (t80) cc_final: 0.6360 (t80) REVERT: C 494 SER cc_start: 0.8384 (t) cc_final: 0.8165 (p) REVERT: A 41 GLN cc_start: 0.7786 (tt0) cc_final: 0.7381 (tt0) REVERT: A 52 LEU cc_start: 0.8750 (tp) cc_final: 0.8471 (tp) REVERT: A 92 THR cc_start: 0.8803 (OUTLIER) cc_final: 0.8379 (p) REVERT: B 72 THR cc_start: 0.8303 (m) cc_final: 0.8083 (p) outliers start: 16 outliers final: 5 residues processed: 108 average time/residue: 0.4880 time to fit residues: 56.6269 Evaluate side-chains 103 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 96 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain A residue 92 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 25 optimal weight: 0.4980 chunk 10 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 36 optimal weight: 0.2980 chunk 12 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 388 ASN C 409 GLN C 506 GLN A 78 ASN B 33 ASN B 41 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 3389 Z= 0.436 Angle : 0.688 11.559 4619 Z= 0.341 Chirality : 0.047 0.237 516 Planarity : 0.005 0.063 590 Dihedral : 6.051 45.885 477 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.09 % Favored : 87.91 % Rotamer: Outliers : 5.19 % Allowed : 15.03 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -3.09 (0.39), residues: 422 helix: -5.19 (0.24), residues: 12 sheet: -1.25 (0.41), residues: 146 loop : -2.49 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 49 HIS 0.002 0.001 HIS B 41 PHE 0.022 0.002 PHE A 24 TYR 0.020 0.002 TYR C 380 ARG 0.003 0.001 ARG C 509 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 99 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: C 346 ARG cc_start: 0.7048 (tpt90) cc_final: 0.6641 (tpt90) REVERT: C 395 VAL cc_start: 0.8789 (OUTLIER) cc_final: 0.8386 (m) REVERT: C 399 SER cc_start: 0.8424 (m) cc_final: 0.8195 (p) REVERT: C 407 VAL cc_start: 0.8700 (t) cc_final: 0.8484 (p) REVERT: C 429 PHE cc_start: 0.7699 (t80) cc_final: 0.7415 (t80) REVERT: C 438 SER cc_start: 0.8592 (p) cc_final: 0.8313 (p) REVERT: C 473 TYR cc_start: 0.6756 (t80) cc_final: 0.6496 (t80) REVERT: C 503 VAL cc_start: 0.8485 (t) cc_final: 0.8123 (p) REVERT: C 512 VAL cc_start: 0.8193 (m) cc_final: 0.7887 (p) REVERT: A 20 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7970 (mm) REVERT: A 41 GLN cc_start: 0.7790 (tt0) cc_final: 0.7510 (tt0) REVERT: A 92 THR cc_start: 0.8854 (OUTLIER) cc_final: 0.8509 (p) REVERT: A 96 TYR cc_start: 0.8389 (m-80) cc_final: 0.8167 (m-80) REVERT: B 78 SER cc_start: 0.7872 (t) cc_final: 0.7489 (p) REVERT: B 83 GLU cc_start: 0.7421 (mp0) cc_final: 0.6987 (mp0) REVERT: B 98 VAL cc_start: 0.8632 (t) cc_final: 0.8402 (p) outliers start: 19 outliers final: 8 residues processed: 109 average time/residue: 0.4493 time to fit residues: 52.4368 Evaluate side-chains 111 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 100 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 55 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.0370 chunk 28 optimal weight: 0.6980 chunk 19 optimal weight: 0.3980 chunk 4 optimal weight: 0.2980 chunk 17 optimal weight: 0.1980 chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 39 optimal weight: 0.0980 chunk 35 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 33 optimal weight: 0.2980 overall best weight: 0.1858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 409 GLN C 414 GLN A 78 ASN A 112 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3389 Z= 0.161 Angle : 0.602 10.163 4619 Z= 0.284 Chirality : 0.043 0.211 516 Planarity : 0.005 0.057 590 Dihedral : 5.111 36.508 474 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 3.55 % Allowed : 17.76 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -2.74 (0.39), residues: 422 helix: -5.08 (0.28), residues: 12 sheet: -0.95 (0.42), residues: 143 loop : -2.27 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.000 0.000 HIS B 41 PHE 0.008 0.001 PHE C 429 TYR 0.016 0.001 TYR B 51 ARG 0.002 0.000 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 96 time to evaluate : 0.380 Fit side-chains REVERT: C 341 VAL cc_start: 0.8820 (m) cc_final: 0.8580 (p) REVERT: C 346 ARG cc_start: 0.6986 (tpt90) cc_final: 0.6587 (tpt90) REVERT: C 392 PHE cc_start: 0.8436 (m-80) cc_final: 0.7993 (m-80) REVERT: C 395 VAL cc_start: 0.8760 (OUTLIER) cc_final: 0.8388 (m) REVERT: C 399 SER cc_start: 0.8436 (m) cc_final: 0.8232 (p) REVERT: C 407 VAL cc_start: 0.8658 (t) cc_final: 0.8438 (p) REVERT: C 429 PHE cc_start: 0.7624 (t80) cc_final: 0.7385 (t80) REVERT: C 438 SER cc_start: 0.8500 (p) cc_final: 0.8204 (p) REVERT: C 494 SER cc_start: 0.8568 (t) cc_final: 0.8333 (p) REVERT: C 503 VAL cc_start: 0.8331 (t) cc_final: 0.7934 (p) REVERT: C 512 VAL cc_start: 0.8129 (m) cc_final: 0.7831 (p) REVERT: A 20 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7902 (mm) REVERT: A 92 THR cc_start: 0.8782 (OUTLIER) cc_final: 0.8467 (p) REVERT: A 96 TYR cc_start: 0.8364 (m-80) cc_final: 0.8084 (m-80) REVERT: B 55 LYS cc_start: 0.7226 (OUTLIER) cc_final: 0.6826 (mptp) REVERT: B 83 GLU cc_start: 0.7225 (mp0) cc_final: 0.6842 (mp0) outliers start: 13 outliers final: 6 residues processed: 104 average time/residue: 0.4997 time to fit residues: 55.3667 Evaluate side-chains 106 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 96 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 55 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 chunk 16 optimal weight: 0.1980 chunk 33 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 0.4980 chunk 35 optimal weight: 0.0000 chunk 10 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 0.4980 overall best weight: 0.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 409 GLN C 506 GLN A 78 ASN A 112 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3389 Z= 0.241 Angle : 0.630 11.057 4619 Z= 0.297 Chirality : 0.043 0.193 516 Planarity : 0.005 0.058 590 Dihedral : 5.211 36.267 474 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.43 % Favored : 89.57 % Rotamer: Outliers : 4.64 % Allowed : 19.40 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -2.46 (0.40), residues: 422 helix: -5.06 (0.29), residues: 12 sheet: -0.78 (0.42), residues: 150 loop : -2.07 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 436 HIS 0.001 0.000 HIS B 41 PHE 0.030 0.002 PHE C 342 TYR 0.015 0.001 TYR B 51 ARG 0.001 0.000 ARG A 60 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 96 time to evaluate : 0.377 Fit side-chains REVERT: C 341 VAL cc_start: 0.8757 (m) cc_final: 0.8547 (p) REVERT: C 346 ARG cc_start: 0.6981 (tpt90) cc_final: 0.6568 (tpt90) REVERT: C 358 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.7957 (pt) REVERT: C 392 PHE cc_start: 0.8441 (m-80) cc_final: 0.7979 (m-80) REVERT: C 395 VAL cc_start: 0.8768 (OUTLIER) cc_final: 0.8345 (p) REVERT: C 399 SER cc_start: 0.8456 (m) cc_final: 0.8219 (p) REVERT: C 407 VAL cc_start: 0.8674 (t) cc_final: 0.8442 (p) REVERT: C 429 PHE cc_start: 0.7676 (t80) cc_final: 0.7470 (t80) REVERT: C 438 SER cc_start: 0.8518 (p) cc_final: 0.8227 (p) REVERT: C 473 TYR cc_start: 0.6589 (t80) cc_final: 0.6200 (t80) REVERT: C 503 VAL cc_start: 0.8374 (t) cc_final: 0.7988 (p) REVERT: A 17 THR cc_start: 0.7656 (p) cc_final: 0.7408 (m) REVERT: A 20 LEU cc_start: 0.8126 (mt) cc_final: 0.7911 (mm) REVERT: A 41 GLN cc_start: 0.7633 (tt0) cc_final: 0.7290 (tt0) REVERT: A 92 THR cc_start: 0.8829 (OUTLIER) cc_final: 0.8496 (p) REVERT: B 55 LYS cc_start: 0.7295 (OUTLIER) cc_final: 0.6896 (mptp) REVERT: B 78 SER cc_start: 0.7688 (t) cc_final: 0.7269 (p) REVERT: B 83 GLU cc_start: 0.7291 (mp0) cc_final: 0.6856 (mp0) outliers start: 17 outliers final: 6 residues processed: 106 average time/residue: 0.4633 time to fit residues: 52.5474 Evaluate side-chains 104 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 55 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.2980 chunk 9 optimal weight: 0.2980 chunk 39 optimal weight: 0.0980 chunk 32 optimal weight: 0.4980 chunk 18 optimal weight: 0.0270 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 0.2980 chunk 20 optimal weight: 0.2980 chunk 38 optimal weight: 0.9980 chunk 4 optimal weight: 0.0970 chunk 22 optimal weight: 0.9980 overall best weight: 0.1636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 409 GLN C 506 GLN A 78 ASN A 112 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3389 Z= 0.152 Angle : 0.613 11.011 4619 Z= 0.282 Chirality : 0.042 0.176 516 Planarity : 0.005 0.056 590 Dihedral : 5.058 34.948 474 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 3.28 % Allowed : 21.31 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -2.41 (0.40), residues: 422 helix: -4.82 (0.32), residues: 20 sheet: -0.37 (0.44), residues: 139 loop : -2.14 (0.38), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.000 0.000 HIS B 41 PHE 0.028 0.001 PHE C 342 TYR 0.017 0.001 TYR B 51 ARG 0.001 0.000 ARG A 60 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 97 time to evaluate : 0.372 Fit side-chains REVERT: C 346 ARG cc_start: 0.6938 (tpt90) cc_final: 0.6558 (tpt90) REVERT: C 358 ILE cc_start: 0.8308 (OUTLIER) cc_final: 0.7949 (pt) REVERT: C 395 VAL cc_start: 0.8708 (OUTLIER) cc_final: 0.8305 (p) REVERT: C 407 VAL cc_start: 0.8544 (t) cc_final: 0.8337 (p) REVERT: C 429 PHE cc_start: 0.7642 (t80) cc_final: 0.7401 (t80) REVERT: C 438 SER cc_start: 0.8482 (p) cc_final: 0.8167 (p) REVERT: C 473 TYR cc_start: 0.6573 (t80) cc_final: 0.6177 (t80) REVERT: C 494 SER cc_start: 0.8566 (t) cc_final: 0.8342 (p) REVERT: C 503 VAL cc_start: 0.8288 (t) cc_final: 0.7900 (p) REVERT: A 17 THR cc_start: 0.7681 (p) cc_final: 0.7429 (m) REVERT: A 20 LEU cc_start: 0.8118 (mt) cc_final: 0.7916 (mm) REVERT: A 92 THR cc_start: 0.8773 (OUTLIER) cc_final: 0.8463 (p) REVERT: B 55 LYS cc_start: 0.7200 (OUTLIER) cc_final: 0.6735 (mptp) REVERT: B 83 GLU cc_start: 0.7131 (mp0) cc_final: 0.6755 (mp0) outliers start: 12 outliers final: 5 residues processed: 103 average time/residue: 0.4531 time to fit residues: 49.9778 Evaluate side-chains 105 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 96 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 55 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 506 GLN A 78 ASN A 112 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 3389 Z= 0.425 Angle : 0.697 12.932 4619 Z= 0.337 Chirality : 0.046 0.189 516 Planarity : 0.005 0.061 590 Dihedral : 5.617 36.772 474 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.61 % Favored : 88.39 % Rotamer: Outliers : 4.10 % Allowed : 21.86 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -2.44 (0.40), residues: 422 helix: -4.74 (0.36), residues: 20 sheet: -0.66 (0.43), residues: 153 loop : -2.05 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 436 HIS 0.001 0.000 HIS C 505 PHE 0.016 0.002 PHE C 400 TYR 0.017 0.002 TYR C 453 ARG 0.002 0.000 ARG A 60 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 105 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: C 346 ARG cc_start: 0.6996 (tpt90) cc_final: 0.6558 (tpt90) REVERT: C 395 VAL cc_start: 0.8753 (OUTLIER) cc_final: 0.8392 (m) REVERT: C 399 SER cc_start: 0.8537 (m) cc_final: 0.8133 (p) REVERT: C 407 VAL cc_start: 0.8710 (t) cc_final: 0.8464 (p) REVERT: C 429 PHE cc_start: 0.7778 (t80) cc_final: 0.7527 (t80) REVERT: C 438 SER cc_start: 0.8625 (p) cc_final: 0.8367 (p) REVERT: C 473 TYR cc_start: 0.6557 (t80) cc_final: 0.6175 (t80) REVERT: C 503 VAL cc_start: 0.8528 (t) cc_final: 0.8180 (p) REVERT: A 10 THR cc_start: 0.8679 (p) cc_final: 0.8249 (t) REVERT: A 18 LEU cc_start: 0.7808 (mt) cc_final: 0.7486 (mt) REVERT: A 20 LEU cc_start: 0.8162 (mt) cc_final: 0.7892 (mm) REVERT: A 31 THR cc_start: 0.8574 (OUTLIER) cc_final: 0.8100 (p) REVERT: A 92 THR cc_start: 0.8840 (OUTLIER) cc_final: 0.8524 (p) REVERT: A 96 TYR cc_start: 0.8405 (m-80) cc_final: 0.8202 (m-80) REVERT: B 83 GLU cc_start: 0.7389 (mp0) cc_final: 0.6922 (mp0) outliers start: 15 outliers final: 11 residues processed: 113 average time/residue: 0.4955 time to fit residues: 59.5710 Evaluate side-chains 109 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 95 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 55 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 0.0970 chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 35 optimal weight: 0.1980 chunk 37 optimal weight: 0.9990 chunk 34 optimal weight: 0.3980 chunk 36 optimal weight: 0.2980 chunk 22 optimal weight: 0.5980 chunk 16 optimal weight: 0.0170 chunk 28 optimal weight: 0.6980 overall best weight: 0.2016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 506 GLN A 78 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3389 Z= 0.178 Angle : 0.622 11.406 4619 Z= 0.293 Chirality : 0.043 0.170 516 Planarity : 0.005 0.058 590 Dihedral : 5.324 38.650 474 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 4.92 % Allowed : 21.86 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -2.22 (0.41), residues: 422 helix: -4.61 (0.43), residues: 20 sheet: -0.45 (0.44), residues: 150 loop : -1.92 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 436 HIS 0.001 0.000 HIS B 41 PHE 0.015 0.001 PHE A 24 TYR 0.016 0.001 TYR B 51 ARG 0.001 0.000 ARG C 498 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 96 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: C 395 VAL cc_start: 0.8740 (OUTLIER) cc_final: 0.8382 (m) REVERT: C 407 VAL cc_start: 0.8676 (t) cc_final: 0.8438 (p) REVERT: C 429 PHE cc_start: 0.7701 (t80) cc_final: 0.7425 (t80) REVERT: C 438 SER cc_start: 0.8523 (p) cc_final: 0.8208 (p) REVERT: C 473 TYR cc_start: 0.6502 (t80) cc_final: 0.6157 (t80) REVERT: C 503 VAL cc_start: 0.8358 (t) cc_final: 0.7984 (p) REVERT: A 92 THR cc_start: 0.8802 (OUTLIER) cc_final: 0.8510 (p) REVERT: A 96 TYR cc_start: 0.8357 (m-80) cc_final: 0.8125 (m-80) REVERT: A 114 THR cc_start: 0.8351 (p) cc_final: 0.8119 (t) REVERT: B 55 LYS cc_start: 0.7340 (OUTLIER) cc_final: 0.6959 (mptp) REVERT: B 83 GLU cc_start: 0.7200 (mp0) cc_final: 0.6807 (mp0) outliers start: 18 outliers final: 8 residues processed: 106 average time/residue: 0.5112 time to fit residues: 57.6777 Evaluate side-chains 106 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 95 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 55 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 0.0050 chunk 34 optimal weight: 0.7980 chunk 36 optimal weight: 0.0770 chunk 24 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 23 optimal weight: 0.4980 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 37 optimal weight: 0.0970 overall best weight: 0.2550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 409 GLN C 506 GLN A 78 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3389 Z= 0.197 Angle : 0.642 12.081 4619 Z= 0.298 Chirality : 0.043 0.156 516 Planarity : 0.005 0.058 590 Dihedral : 5.181 34.083 474 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.95 % Favored : 90.05 % Rotamer: Outliers : 3.28 % Allowed : 23.77 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -2.09 (0.41), residues: 422 helix: -4.44 (0.55), residues: 20 sheet: -0.35 (0.44), residues: 150 loop : -1.85 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 436 HIS 0.000 0.000 HIS B 41 PHE 0.008 0.001 PHE C 342 TYR 0.015 0.001 TYR B 51 ARG 0.001 0.000 ARG C 457 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: C 392 PHE cc_start: 0.8443 (m-80) cc_final: 0.8080 (m-80) REVERT: C 395 VAL cc_start: 0.8727 (OUTLIER) cc_final: 0.8382 (m) REVERT: C 399 SER cc_start: 0.8512 (m) cc_final: 0.8088 (p) REVERT: C 407 VAL cc_start: 0.8502 (t) cc_final: 0.8290 (p) REVERT: C 429 PHE cc_start: 0.7707 (t80) cc_final: 0.7444 (t80) REVERT: C 473 TYR cc_start: 0.6513 (t80) cc_final: 0.6162 (t80) REVERT: C 503 VAL cc_start: 0.8364 (t) cc_final: 0.7980 (p) REVERT: A 92 THR cc_start: 0.8821 (OUTLIER) cc_final: 0.8519 (p) REVERT: A 96 TYR cc_start: 0.8375 (m-80) cc_final: 0.8120 (m-80) REVERT: B 55 LYS cc_start: 0.7330 (OUTLIER) cc_final: 0.6941 (mptp) REVERT: B 83 GLU cc_start: 0.7211 (mp0) cc_final: 0.6778 (mp0) outliers start: 12 outliers final: 8 residues processed: 104 average time/residue: 0.5132 time to fit residues: 56.7648 Evaluate side-chains 107 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 55 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.0980 chunk 34 optimal weight: 0.0870 chunk 9 optimal weight: 0.0670 chunk 29 optimal weight: 0.7980 chunk 4 optimal weight: 0.3980 chunk 13 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 chunk 6 optimal weight: 0.4980 overall best weight: 0.2296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 409 GLN C 506 GLN A 78 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3389 Z= 0.185 Angle : 0.634 12.540 4619 Z= 0.296 Chirality : 0.043 0.150 516 Planarity : 0.005 0.057 590 Dihedral : 5.177 34.647 474 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 3.28 % Allowed : 24.04 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.41), residues: 422 helix: -4.45 (0.54), residues: 20 sheet: -0.27 (0.44), residues: 150 loop : -1.79 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 436 HIS 0.001 0.000 HIS B 41 PHE 0.015 0.002 PHE C 400 TYR 0.016 0.001 TYR B 51 ARG 0.001 0.000 ARG C 509 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 97 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: C 392 PHE cc_start: 0.8430 (m-80) cc_final: 0.8067 (m-80) REVERT: C 395 VAL cc_start: 0.8707 (OUTLIER) cc_final: 0.8362 (m) REVERT: C 399 SER cc_start: 0.8505 (m) cc_final: 0.8093 (p) REVERT: C 407 VAL cc_start: 0.8505 (t) cc_final: 0.8288 (p) REVERT: C 429 PHE cc_start: 0.7708 (t80) cc_final: 0.7453 (t80) REVERT: C 473 TYR cc_start: 0.6558 (t80) cc_final: 0.6172 (t80) REVERT: C 503 VAL cc_start: 0.8361 (t) cc_final: 0.7977 (p) REVERT: A 92 THR cc_start: 0.8819 (OUTLIER) cc_final: 0.8513 (p) REVERT: A 96 TYR cc_start: 0.8375 (m-80) cc_final: 0.8119 (m-80) REVERT: B 55 LYS cc_start: 0.7288 (OUTLIER) cc_final: 0.6852 (mptp) REVERT: B 83 GLU cc_start: 0.7164 (mp0) cc_final: 0.6729 (mp0) outliers start: 12 outliers final: 8 residues processed: 105 average time/residue: 0.4540 time to fit residues: 51.0723 Evaluate side-chains 97 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 86 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 55 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.9990 chunk 1 optimal weight: 0.2980 chunk 23 optimal weight: 0.4980 chunk 37 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 0.0370 chunk 24 optimal weight: 0.1980 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 40 optimal weight: 0.4980 overall best weight: 0.3058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 409 GLN C 450 ASN C 506 GLN A 78 ASN A 112 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.132770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.121300 restraints weight = 5163.769| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.36 r_work: 0.3514 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3389 Z= 0.225 Angle : 0.659 12.546 4619 Z= 0.307 Chirality : 0.043 0.138 516 Planarity : 0.005 0.058 590 Dihedral : 5.193 32.197 474 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.95 % Favored : 90.05 % Rotamer: Outliers : 3.83 % Allowed : 24.32 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -2.01 (0.41), residues: 422 helix: -4.42 (0.56), residues: 20 sheet: -0.26 (0.44), residues: 150 loop : -1.82 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 436 HIS 0.000 0.000 HIS B 41 PHE 0.015 0.001 PHE C 342 TYR 0.016 0.001 TYR C 453 ARG 0.001 0.000 ARG C 457 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1898.52 seconds wall clock time: 34 minutes 32.37 seconds (2072.37 seconds total)