Starting phenix.real_space_refine on Wed Mar 5 18:49:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yd1_33745/03_2025/7yd1_33745.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yd1_33745/03_2025/7yd1_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/cci-nas-00/data/ceres_data/7yd1_33745/03_2025/7yd1_33745.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yd1_33745/03_2025/7yd1_33745.map" model { file = "/net/cci-nas-00/data/ceres_data/7yd1_33745/03_2025/7yd1_33745.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yd1_33745/03_2025/7yd1_33745.cif" } 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. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 3.22, per 1000 atoms: 0.97 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 - 3.00 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: 0.87 Conformation dependent library (CDL) restraints added in 444.5 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: 0.45 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: 0.82 Time building geometry restraints manager: 1.04 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: 0.00 - 1.82: 4552 1.82 - 3.63: 63 3.63 - 5.45: 3 5.45 - 7.26: 0 7.26 - 9.08: 1 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 3.040 nonbonded pdb=" OG1 THR B 5 " pdb=" OG1 THR B 23 " model vdw 2.276 3.040 nonbonded pdb=" OG1 THR A 70 " pdb=" OG1 THR A 83 " model vdw 2.289 3.040 nonbonded pdb=" O ILE A 106 " pdb=" OH TYR B 38 " model vdw 2.308 3.040 nonbonded pdb=" O THR C 393 " pdb=" OG1 THR C 523 " model vdw 2.310 3.040 ... (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 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: 2.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.100 Find NCS groups from input model: 0.040 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:12.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.290 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.398 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: 0.5056 time to fit residues: 66.5967 Evaluate side-chains 107 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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: 0.7980 chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 16 optimal weight: 0.4980 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 0.0980 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 0.0770 chunk 37 optimal weight: 0.9980 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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 460 ASN C 506 GLN A 16 GLN A 78 ASN A 79 GLN B 39 GLN B 41 HIS B 81 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.133218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.121508 restraints weight = 5068.965| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.37 r_work: 0.3509 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 3389 Z= 0.323 Angle : 0.645 11.567 4619 Z= 0.323 Chirality : 0.045 0.211 516 Planarity : 0.005 0.058 590 Dihedral : 5.801 45.312 479 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.61 % Favored : 88.39 % Rotamer: Outliers : 4.92 % Allowed : 12.57 % Favored : 82.51 % 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: -3.37 (0.38), residues: 422 helix: -5.23 (0.23), residues: 12 sheet: -1.45 (0.41), residues: 146 loop : -2.69 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 49 HIS 0.001 0.000 HIS B 41 PHE 0.011 0.001 PHE A 24 TYR 0.016 0.002 TYR B 51 ARG 0.003 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 123 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.377 Fit side-chains REVERT: C 346 ARG cc_start: 0.7633 (tpt90) cc_final: 0.7232 (tpt90) REVERT: C 351 TYR cc_start: 0.8338 (p90) cc_final: 0.8090 (p90) REVERT: C 395 VAL cc_start: 0.8852 (OUTLIER) cc_final: 0.8472 (m) REVERT: C 399 SER cc_start: 0.8689 (m) cc_final: 0.8437 (p) REVERT: C 407 VAL cc_start: 0.8771 (t) cc_final: 0.8567 (p) REVERT: C 429 PHE cc_start: 0.7878 (t80) cc_final: 0.7558 (t80) REVERT: C 438 SER cc_start: 0.8727 (p) cc_final: 0.8460 (p) REVERT: C 445 VAL cc_start: 0.8651 (t) cc_final: 0.8437 (m) REVERT: C 456 PHE cc_start: 0.7620 (m-80) cc_final: 0.7416 (m-80) REVERT: C 473 TYR cc_start: 0.6982 (t80) cc_final: 0.6615 (t80) REVERT: C 494 SER cc_start: 0.8526 (t) cc_final: 0.8308 (p) REVERT: A 18 LEU cc_start: 0.7877 (mt) cc_final: 0.7377 (mp) REVERT: A 41 GLN cc_start: 0.8350 (tt0) cc_final: 0.8002 (tt0) REVERT: A 52 LEU cc_start: 0.9002 (tp) cc_final: 0.8762 (tp) REVERT: A 92 THR cc_start: 0.8959 (OUTLIER) cc_final: 0.8636 (p) REVERT: A 107 PHE cc_start: 0.8236 (m-10) cc_final: 0.7979 (m-10) REVERT: B 20 ILE cc_start: 0.7934 (OUTLIER) cc_final: 0.7682 (mm) REVERT: B 55 LYS cc_start: 0.7392 (OUTLIER) cc_final: 0.6972 (mptp) REVERT: B 63 ARG cc_start: 0.8586 (mtp180) cc_final: 0.8325 (mtp180) REVERT: B 83 GLU cc_start: 0.7917 (mp0) cc_final: 0.7483 (mp0) outliers start: 18 outliers final: 7 residues processed: 112 average time/residue: 0.4649 time to fit residues: 55.6715 Evaluate side-chains 103 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 C residue 528 LYS Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 55 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 40 optimal weight: 0.0370 chunk 13 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 34 optimal weight: 0.2980 chunk 28 optimal weight: 0.2980 chunk 32 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.0670 chunk 0 optimal weight: 1.9990 chunk 37 optimal weight: 0.0370 overall best weight: 0.1474 ------------------------------------------------------------------------------- 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 B 33 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.134851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.123545 restraints weight = 5095.887| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.39 r_work: 0.3536 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3389 Z= 0.147 Angle : 0.577 9.872 4619 Z= 0.280 Chirality : 0.043 0.223 516 Planarity : 0.005 0.054 590 Dihedral : 5.367 42.745 477 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 4.10 % Allowed : 16.39 % Favored : 79.51 % 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: -3.03 (0.39), residues: 422 helix: -4.99 (0.27), residues: 20 sheet: -0.98 (0.42), residues: 142 loop : -2.49 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.001 0.000 HIS B 41 PHE 0.021 0.001 PHE A 24 TYR 0.017 0.001 TYR B 51 ARG 0.002 0.000 ARG C 457 *********************** 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 109 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.387 Fit side-chains REVERT: C 395 VAL cc_start: 0.8833 (OUTLIER) cc_final: 0.8494 (m) REVERT: C 396 TYR cc_start: 0.7892 (m-10) cc_final: 0.7594 (m-80) REVERT: C 399 SER cc_start: 0.8701 (m) cc_final: 0.8499 (p) REVERT: C 407 VAL cc_start: 0.8734 (t) cc_final: 0.8516 (p) REVERT: C 429 PHE cc_start: 0.7885 (t80) cc_final: 0.7576 (t80) REVERT: C 438 SER cc_start: 0.8654 (p) cc_final: 0.8372 (p) REVERT: C 445 VAL cc_start: 0.8689 (t) cc_final: 0.8470 (m) REVERT: C 456 PHE cc_start: 0.7602 (m-80) cc_final: 0.7337 (m-80) REVERT: C 473 TYR cc_start: 0.6970 (t80) cc_final: 0.6712 (t80) REVERT: C 494 SER cc_start: 0.8481 (t) cc_final: 0.8240 (p) REVERT: C 511 VAL cc_start: 0.8342 (OUTLIER) cc_final: 0.8102 (t) REVERT: A 18 LEU cc_start: 0.7645 (mt) cc_final: 0.7157 (mp) REVERT: A 52 LEU cc_start: 0.8966 (tp) cc_final: 0.8763 (tp) REVERT: B 55 LYS cc_start: 0.7229 (OUTLIER) cc_final: 0.6767 (mptp) REVERT: B 83 GLU cc_start: 0.7796 (mp0) cc_final: 0.7350 (mp0) outliers start: 15 outliers final: 8 residues processed: 101 average time/residue: 0.5704 time to fit residues: 61.0604 Evaluate side-chains 110 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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 382 VAL Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 92 THR 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 30 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 25 optimal weight: 0.4980 chunk 5 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 23 optimal weight: 0.0970 chunk 22 optimal weight: 0.6980 chunk 9 optimal weight: 0.0970 chunk 19 optimal weight: 0.2980 overall best weight: 0.3176 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.131838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.120312 restraints weight = 5155.456| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.39 r_work: 0.3509 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 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 : 0.004 0.043 3389 Z= 0.225 Angle : 0.601 10.366 4619 Z= 0.289 Chirality : 0.043 0.189 516 Planarity : 0.005 0.056 590 Dihedral : 5.457 43.295 477 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 4.64 % Allowed : 17.49 % Favored : 77.87 % 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: -2.65 (0.40), residues: 422 helix: -5.11 (0.27), residues: 12 sheet: -0.83 (0.42), residues: 144 loop : -2.24 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 49 HIS 0.001 0.000 HIS B 41 PHE 0.019 0.001 PHE A 24 TYR 0.016 0.001 TYR B 51 ARG 0.001 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 114 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.387 Fit side-chains REVERT: C 395 VAL cc_start: 0.8834 (OUTLIER) cc_final: 0.8501 (m) REVERT: C 396 TYR cc_start: 0.7918 (m-10) cc_final: 0.7585 (m-80) REVERT: C 407 VAL cc_start: 0.8728 (t) cc_final: 0.8496 (p) REVERT: C 429 PHE cc_start: 0.7946 (t80) cc_final: 0.7620 (t80) REVERT: C 438 SER cc_start: 0.8674 (p) cc_final: 0.8386 (p) REVERT: C 445 VAL cc_start: 0.8654 (t) cc_final: 0.8441 (m) REVERT: C 456 PHE cc_start: 0.7648 (m-80) cc_final: 0.7386 (m-80) REVERT: C 494 SER cc_start: 0.8534 (t) cc_final: 0.8312 (p) REVERT: A 18 LEU cc_start: 0.7859 (mt) cc_final: 0.7343 (mp) REVERT: A 52 LEU cc_start: 0.9006 (tp) cc_final: 0.8774 (tp) REVERT: A 92 THR cc_start: 0.8936 (OUTLIER) cc_final: 0.8596 (p) REVERT: B 20 ILE cc_start: 0.7972 (OUTLIER) cc_final: 0.7738 (mm) REVERT: B 55 LYS cc_start: 0.7441 (OUTLIER) cc_final: 0.6953 (mptp) REVERT: B 63 ARG cc_start: 0.8612 (mtp180) cc_final: 0.8368 (mtp180) REVERT: B 83 GLU cc_start: 0.8003 (mp0) cc_final: 0.7479 (mp0) outliers start: 17 outliers final: 6 residues processed: 107 average time/residue: 0.5011 time to fit residues: 57.1779 Evaluate side-chains 109 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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 68 SER Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 20 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 10 optimal weight: 0.0370 chunk 16 optimal weight: 0.8980 chunk 17 optimal weight: 0.4980 chunk 3 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 22 optimal weight: 0.3980 chunk 36 optimal weight: 0.0670 overall best weight: 0.3196 ------------------------------------------------------------------------------- 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 C 450 ASN C 506 GLN A 78 ASN B 40 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.132286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.121098 restraints weight = 5131.295| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.30 r_work: 0.3509 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3389 Z= 0.222 Angle : 0.611 10.970 4619 Z= 0.291 Chirality : 0.043 0.210 516 Planarity : 0.005 0.057 590 Dihedral : 5.565 42.357 477 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 3.28 % Allowed : 19.13 % Favored : 77.60 % 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: -2.50 (0.40), residues: 422 helix: -5.03 (0.30), residues: 12 sheet: -0.67 (0.42), residues: 143 loop : -2.17 (0.38), residues: 267 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 0.008 0.001 PHE A 107 TYR 0.014 0.001 TYR B 51 ARG 0.001 0.000 ARG C 457 *********************** 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 112 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.421 Fit side-chains REVERT: C 395 VAL cc_start: 0.8830 (OUTLIER) cc_final: 0.8486 (m) REVERT: C 407 VAL cc_start: 0.8753 (t) cc_final: 0.8530 (p) REVERT: C 429 PHE cc_start: 0.7944 (t80) cc_final: 0.7569 (t80) REVERT: C 438 SER cc_start: 0.8645 (p) cc_final: 0.8359 (p) REVERT: C 445 VAL cc_start: 0.8658 (t) cc_final: 0.8434 (m) REVERT: C 456 PHE cc_start: 0.7654 (m-80) cc_final: 0.7437 (m-80) REVERT: C 473 TYR cc_start: 0.6851 (t80) cc_final: 0.6394 (t80) REVERT: C 494 SER cc_start: 0.8560 (t) cc_final: 0.8307 (p) REVERT: C 512 VAL cc_start: 0.8461 (m) cc_final: 0.8192 (p) REVERT: A 92 THR cc_start: 0.8942 (OUTLIER) cc_final: 0.8602 (p) REVERT: B 55 LYS cc_start: 0.7462 (OUTLIER) cc_final: 0.7022 (mptp) REVERT: B 63 ARG cc_start: 0.8598 (mtp180) cc_final: 0.8354 (mtp180) REVERT: B 83 GLU cc_start: 0.8007 (mp0) cc_final: 0.7432 (mp0) outliers start: 12 outliers final: 5 residues processed: 107 average time/residue: 0.4834 time to fit residues: 55.3033 Evaluate side-chains 105 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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 393 THR Chi-restraints excluded: chain C residue 395 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 15 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 13 optimal weight: 0.0270 chunk 28 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 overall best weight: 0.4838 ------------------------------------------------------------------------------- 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 C 506 GLN A 78 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.129864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.118229 restraints weight = 5289.680| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.40 r_work: 0.3473 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 3389 Z= 0.319 Angle : 0.660 11.771 4619 Z= 0.319 Chirality : 0.045 0.212 516 Planarity : 0.005 0.059 590 Dihedral : 5.428 33.716 475 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer: Outliers : 4.10 % Allowed : 20.77 % Favored : 75.14 % 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: -2.42 (0.40), residues: 422 helix: -5.06 (0.29), residues: 12 sheet: -0.70 (0.42), residues: 146 loop : -2.07 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 49 HIS 0.001 0.000 HIS B 41 PHE 0.030 0.002 PHE C 342 TYR 0.017 0.002 TYR C 380 ARG 0.002 0.000 ARG C 408 *********************** 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 115 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.380 Fit side-chains REVERT: C 395 VAL cc_start: 0.8831 (OUTLIER) cc_final: 0.8473 (m) REVERT: C 407 VAL cc_start: 0.8768 (t) cc_final: 0.8548 (p) REVERT: C 429 PHE cc_start: 0.8001 (t80) cc_final: 0.7685 (t80) REVERT: C 438 SER cc_start: 0.8698 (p) cc_final: 0.8404 (p) REVERT: C 445 VAL cc_start: 0.8645 (t) cc_final: 0.8420 (m) REVERT: C 473 TYR cc_start: 0.6838 (t80) cc_final: 0.6417 (t80) REVERT: C 494 SER cc_start: 0.8666 (t) cc_final: 0.8422 (p) REVERT: C 503 VAL cc_start: 0.8659 (t) cc_final: 0.8256 (p) REVERT: A 52 LEU cc_start: 0.9033 (tp) cc_final: 0.8815 (tp) REVERT: A 92 THR cc_start: 0.8951 (OUTLIER) cc_final: 0.8629 (p) REVERT: B 55 LYS cc_start: 0.7529 (OUTLIER) cc_final: 0.7113 (mptp) REVERT: B 63 ARG cc_start: 0.8610 (mtp180) cc_final: 0.8325 (mtp180) REVERT: B 83 GLU cc_start: 0.8174 (mp0) cc_final: 0.7585 (mp0) outliers start: 15 outliers final: 8 residues processed: 109 average time/residue: 0.4793 time to fit residues: 56.2027 Evaluate side-chains 104 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 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 470 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 21 optimal weight: 0.0970 chunk 13 optimal weight: 0.1980 chunk 15 optimal weight: 0.3980 chunk 38 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 17 optimal weight: 0.3980 chunk 30 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 1 optimal weight: 0.4980 overall best weight: 0.3178 ------------------------------------------------------------------------------- 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 C 450 ASN C 506 GLN A 78 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.130979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.119409 restraints weight = 5111.473| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.37 r_work: 0.3486 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3389 Z= 0.230 Angle : 0.645 11.746 4619 Z= 0.304 Chirality : 0.044 0.212 516 Planarity : 0.005 0.057 590 Dihedral : 5.417 39.336 475 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 3.28 % Allowed : 22.13 % Favored : 74.59 % 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: -2.20 (0.41), residues: 422 helix: -5.03 (0.30), residues: 12 sheet: -0.48 (0.43), residues: 140 loop : -1.92 (0.39), residues: 270 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 0.030 0.002 PHE C 342 TYR 0.014 0.001 TYR C 380 ARG 0.002 0.000 ARG C 457 *********************** 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 104 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.393 Fit side-chains REVERT: C 395 VAL cc_start: 0.8785 (OUTLIER) cc_final: 0.8583 (p) REVERT: C 429 PHE cc_start: 0.7985 (t80) cc_final: 0.7640 (t80) REVERT: C 438 SER cc_start: 0.8675 (p) cc_final: 0.8366 (p) REVERT: C 445 VAL cc_start: 0.8655 (t) cc_final: 0.8439 (m) REVERT: C 461 LEU cc_start: 0.8627 (tp) cc_final: 0.8410 (mt) REVERT: C 473 TYR cc_start: 0.6785 (t80) cc_final: 0.6360 (t80) REVERT: C 494 SER cc_start: 0.8602 (t) cc_final: 0.8381 (p) REVERT: C 523 THR cc_start: 0.8042 (p) cc_final: 0.7666 (t) REVERT: A 52 LEU cc_start: 0.9049 (tp) cc_final: 0.8816 (tp) REVERT: A 92 THR cc_start: 0.8938 (OUTLIER) cc_final: 0.8647 (p) REVERT: B 55 LYS cc_start: 0.7478 (OUTLIER) cc_final: 0.7041 (mptp) REVERT: B 63 ARG cc_start: 0.8592 (mtp180) cc_final: 0.8318 (mtp180) REVERT: B 83 GLU cc_start: 0.8100 (mp0) cc_final: 0.7502 (mp0) outliers start: 12 outliers final: 7 residues processed: 100 average time/residue: 0.4418 time to fit residues: 47.5617 Evaluate side-chains 107 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.408 ------------------------------------------------------------------------------- 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 393 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 430 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 6 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 19 optimal weight: 0.4980 chunk 3 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 18 optimal weight: 0.3980 chunk 34 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.129137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.117862 restraints weight = 5155.981| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.30 r_work: 0.3463 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 3389 Z= 0.377 Angle : 0.711 12.706 4619 Z= 0.337 Chirality : 0.046 0.215 516 Planarity : 0.005 0.060 590 Dihedral : 5.587 32.717 475 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.37 % Favored : 88.63 % Rotamer: Outliers : 4.64 % Allowed : 21.58 % Favored : 73.77 % 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: -2.19 (0.41), residues: 422 helix: -5.01 (0.32), residues: 12 sheet: -0.45 (0.43), residues: 140 loop : -1.94 (0.39), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 49 HIS 0.001 0.001 HIS B 41 PHE 0.028 0.002 PHE C 342 TYR 0.019 0.002 TYR C 380 ARG 0.003 0.000 ARG C 457 *********************** 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 120 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.370 Fit side-chains REVERT: C 357 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7752 (ptp-110) REVERT: C 429 PHE cc_start: 0.8051 (t80) cc_final: 0.7733 (t80) REVERT: C 438 SER cc_start: 0.8705 (p) cc_final: 0.8419 (p) REVERT: C 445 VAL cc_start: 0.8675 (t) cc_final: 0.8449 (m) REVERT: C 461 LEU cc_start: 0.8631 (tp) cc_final: 0.8422 (mt) REVERT: C 473 TYR cc_start: 0.6839 (t80) cc_final: 0.6422 (t80) REVERT: C 523 THR cc_start: 0.8109 (p) cc_final: 0.7734 (t) REVERT: A 52 LEU cc_start: 0.9035 (tp) cc_final: 0.8791 (tp) REVERT: A 92 THR cc_start: 0.8962 (OUTLIER) cc_final: 0.8628 (p) REVERT: B 55 LYS cc_start: 0.7543 (OUTLIER) cc_final: 0.7076 (mptp) REVERT: B 63 ARG cc_start: 0.8616 (mtp180) cc_final: 0.8298 (mtp180) REVERT: B 78 SER cc_start: 0.7921 (t) cc_final: 0.7428 (p) REVERT: B 83 GLU cc_start: 0.8173 (mp0) cc_final: 0.7579 (mp0) outliers start: 17 outliers final: 9 residues processed: 113 average time/residue: 0.4844 time to fit residues: 58.2901 Evaluate side-chains 110 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 470 THR 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 53 VAL 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 7 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 1 optimal weight: 0.4980 chunk 17 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 30 optimal weight: 0.4980 chunk 33 optimal weight: 0.0060 chunk 19 optimal weight: 0.4980 chunk 36 optimal weight: 0.0870 chunk 35 optimal weight: 0.3980 overall best weight: 0.2974 ------------------------------------------------------------------------------- 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 86 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.132274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.120734 restraints weight = 5146.435| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.39 r_work: 0.3490 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3389 Z= 0.230 Angle : 0.669 12.313 4619 Z= 0.314 Chirality : 0.044 0.204 516 Planarity : 0.005 0.058 590 Dihedral : 5.211 38.519 472 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 3.55 % Allowed : 21.31 % Favored : 75.14 % 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: -2.02 (0.41), residues: 422 helix: -4.95 (0.36), residues: 12 sheet: -0.40 (0.43), residues: 141 loop : -1.77 (0.40), residues: 269 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 0.019 0.001 PHE C 342 TYR 0.014 0.001 TYR C 453 ARG 0.002 0.000 ARG C 408 *********************** 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 103 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.383 Fit side-chains REVERT: C 351 TYR cc_start: 0.8363 (p90) cc_final: 0.8072 (p90) REVERT: C 429 PHE cc_start: 0.8071 (t80) cc_final: 0.7754 (t80) REVERT: C 438 SER cc_start: 0.8657 (p) cc_final: 0.8345 (p) REVERT: C 445 VAL cc_start: 0.8668 (t) cc_final: 0.8443 (m) REVERT: C 461 LEU cc_start: 0.8638 (tp) cc_final: 0.8426 (mt) REVERT: C 473 TYR cc_start: 0.6812 (t80) cc_final: 0.6439 (t80) REVERT: C 523 THR cc_start: 0.8079 (p) cc_final: 0.7714 (t) REVERT: A 52 LEU cc_start: 0.9043 (tp) cc_final: 0.8787 (tp) REVERT: A 92 THR cc_start: 0.8930 (OUTLIER) cc_final: 0.8644 (p) REVERT: B 55 LYS cc_start: 0.7479 (OUTLIER) cc_final: 0.7002 (mptp) REVERT: B 63 ARG cc_start: 0.8587 (mtp180) cc_final: 0.8311 (mtp180) REVERT: B 83 GLU cc_start: 0.8109 (mp0) cc_final: 0.7494 (mp0) outliers start: 13 outliers final: 7 residues processed: 99 average time/residue: 0.5397 time to fit residues: 56.6568 Evaluate side-chains 99 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 430 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 37 optimal weight: 0.8980 chunk 10 optimal weight: 0.0010 chunk 16 optimal weight: 0.0040 chunk 8 optimal weight: 0.4980 chunk 13 optimal weight: 0.4980 chunk 15 optimal weight: 0.0970 chunk 5 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 25 optimal weight: 0.1980 chunk 14 optimal weight: 0.6980 overall best weight: 0.1596 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.132383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.120959 restraints weight = 5044.342| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.30 r_work: 0.3521 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3389 Z= 0.166 Angle : 0.672 12.202 4619 Z= 0.310 Chirality : 0.044 0.189 516 Planarity : 0.005 0.057 590 Dihedral : 5.073 38.800 472 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 2.19 % Allowed : 23.77 % Favored : 74.04 % 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: -1.93 (0.41), residues: 422 helix: -4.97 (0.32), residues: 12 sheet: -0.26 (0.44), residues: 139 loop : -1.74 (0.39), residues: 271 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 0.010 0.001 PHE C 400 TYR 0.014 0.001 TYR B 51 ARG 0.004 0.000 ARG C 357 ********************** 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 101 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: C 360 ASN cc_start: 0.8389 (m110) cc_final: 0.7894 (m-40) REVERT: C 429 PHE cc_start: 0.8049 (t80) cc_final: 0.7760 (t80) REVERT: C 438 SER cc_start: 0.8642 (p) cc_final: 0.8330 (p) REVERT: C 445 VAL cc_start: 0.8680 (t) cc_final: 0.8459 (m) REVERT: C 473 TYR cc_start: 0.6762 (t80) cc_final: 0.6391 (t80) REVERT: C 523 THR cc_start: 0.8030 (p) cc_final: 0.7706 (t) REVERT: A 87 MET cc_start: 0.6406 (mmm) cc_final: 0.5643 (mmm) REVERT: A 92 THR cc_start: 0.8929 (OUTLIER) cc_final: 0.8658 (p) REVERT: B 55 LYS cc_start: 0.7362 (OUTLIER) cc_final: 0.6905 (mptp) REVERT: B 63 ARG cc_start: 0.8575 (mtp180) cc_final: 0.8075 (mtp180) REVERT: B 83 GLU cc_start: 0.8003 (mp0) cc_final: 0.7415 (mp0) outliers start: 8 outliers final: 5 residues processed: 98 average time/residue: 0.5459 time to fit residues: 56.6851 Evaluate side-chains 97 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 393 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 18 optimal weight: 0.3980 chunk 16 optimal weight: 0.0070 chunk 20 optimal weight: 0.3980 chunk 39 optimal weight: 0.6980 chunk 35 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.3998 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.131059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.119543 restraints weight = 5174.677| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.37 r_work: 0.3492 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 3389 Z= 0.287 Angle : 0.709 13.071 4619 Z= 0.330 Chirality : 0.045 0.193 516 Planarity : 0.005 0.058 590 Dihedral : 5.212 36.542 472 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 3.01 % Allowed : 23.77 % Favored : 73.22 % 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: -1.90 (0.41), residues: 422 helix: -4.91 (0.37), residues: 12 sheet: -0.31 (0.43), residues: 142 loop : -1.70 (0.40), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 436 HIS 0.001 0.000 HIS B 41 PHE 0.013 0.002 PHE A 24 TYR 0.017 0.002 TYR C 423 ARG 0.004 0.000 ARG C 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3069.37 seconds wall clock time: 53 minutes 7.13 seconds (3187.13 seconds total)