Starting phenix.real_space_refine on Fri Dec 27 06:55:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yd1_33745/12_2024/7yd1_33745.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yd1_33745/12_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/cci-nas-00/data/ceres_data/7yd1_33745/12_2024/7yd1_33745.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yd1_33745/12_2024/7yd1_33745.map" model { file = "/net/cci-nas-00/data/ceres_data/7yd1_33745/12_2024/7yd1_33745.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yd1_33745/12_2024/7yd1_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-5532/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: 3.20, 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: 0.80 Conformation dependent library (CDL) restraints added in 456.4 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: 0.41 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: 0.94 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: 1.340 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.290 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.360 ------------------------------------------------------------------------------- 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 : 0.366 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: 0.5177 time to fit residues: 68.2651 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 : 0.338 ------------------------------------------------------------------------------- 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: 0.0060 overall best weight: 0.2954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 409 GLN C 460 ASN C 506 GLN A 16 GLN A 78 ASN A 79 GLN B 39 GLN B 81 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.1699 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= 0.209 Angle : 0.596 10.594 4619 Z= 0.296 Chirality : 0.043 0.199 516 Planarity : 0.005 0.054 590 Dihedral : 5.466 43.874 479 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.95 % Favored : 90.05 % Rotamer: Outliers : 4.92 % Allowed : 12.30 % Favored : 82.79 % 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: -3.48 (0.38), residues: 422 helix: -5.05 (0.25), residues: 20 sheet: -1.35 (0.41), residues: 144 loop : -2.78 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 49 HIS 0.001 0.000 HIS B 41 PHE 0.011 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 122 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.374 Fit side-chains REVERT: C 346 ARG cc_start: 0.6994 (tpt90) cc_final: 0.6750 (tpt90) REVERT: C 392 PHE cc_start: 0.8219 (m-80) cc_final: 0.7900 (m-80) REVERT: C 395 VAL cc_start: 0.8799 (OUTLIER) cc_final: 0.8406 (m) REVERT: C 399 SER cc_start: 0.8402 (m) cc_final: 0.8103 (p) REVERT: C 407 VAL cc_start: 0.8699 (t) cc_final: 0.8473 (p) REVERT: C 429 PHE cc_start: 0.7487 (t80) cc_final: 0.7166 (t80) REVERT: C 438 SER cc_start: 0.8539 (p) cc_final: 0.8258 (p) REVERT: C 445 VAL cc_start: 0.8499 (t) cc_final: 0.8282 (m) REVERT: C 456 PHE cc_start: 0.6802 (m-80) cc_final: 0.6571 (m-80) REVERT: C 473 TYR cc_start: 0.6687 (t80) cc_final: 0.6401 (t80) REVERT: C 494 SER cc_start: 0.8290 (t) cc_final: 0.8063 (p) REVERT: A 18 LEU cc_start: 0.7568 (mt) cc_final: 0.7140 (mp) REVERT: A 41 GLN cc_start: 0.7858 (tt0) cc_final: 0.7448 (tt0) REVERT: A 52 LEU cc_start: 0.8732 (tp) cc_final: 0.8494 (tp) REVERT: A 96 TYR cc_start: 0.8307 (m-80) cc_final: 0.8091 (m-80) REVERT: A 107 PHE cc_start: 0.8159 (m-10) cc_final: 0.7945 (m-10) REVERT: B 63 ARG cc_start: 0.8285 (mtp180) cc_final: 0.8000 (mtp180) REVERT: B 83 GLU cc_start: 0.7114 (mp0) cc_final: 0.6771 (mp0) REVERT: B 84 ASP cc_start: 0.7730 (OUTLIER) cc_final: 0.7508 (m-30) outliers start: 18 outliers final: 7 residues processed: 111 average time/residue: 0.4831 time to fit residues: 57.3668 Evaluate side-chains 108 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 84 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.2980 chunk 11 optimal weight: 0.6980 chunk 30 optimal weight: 0.4980 chunk 25 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 36 optimal weight: 0.0070 chunk 12 optimal weight: 0.8980 chunk 29 optimal weight: 0.4980 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 388 ASN C 409 GLN C 506 GLN B 33 ASN B 41 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3389 Z= 0.271 Angle : 0.626 10.695 4619 Z= 0.306 Chirality : 0.044 0.235 516 Planarity : 0.005 0.058 590 Dihedral : 5.516 45.171 477 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 5.46 % Allowed : 14.75 % Favored : 79.78 % 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: -3.10 (0.39), residues: 422 helix: -4.99 (0.27), residues: 20 sheet: -1.01 (0.42), residues: 142 loop : -2.56 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 49 HIS 0.002 0.000 HIS B 41 PHE 0.022 0.001 PHE A 24 TYR 0.027 0.002 TYR C 380 ARG 0.002 0.000 ARG C 357 *********************** 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 to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.381 Fit side-chains REVERT: C 395 VAL cc_start: 0.8786 (OUTLIER) cc_final: 0.8382 (m) REVERT: C 396 TYR cc_start: 0.7540 (m-80) cc_final: 0.7277 (m-80) REVERT: C 399 SER cc_start: 0.8397 (m) cc_final: 0.8192 (p) REVERT: C 407 VAL cc_start: 0.8665 (t) cc_final: 0.8442 (p) REVERT: C 429 PHE cc_start: 0.7585 (t80) cc_final: 0.7363 (t80) REVERT: C 438 SER cc_start: 0.8568 (p) cc_final: 0.8295 (p) REVERT: C 456 PHE cc_start: 0.7121 (m-80) cc_final: 0.6890 (m-80) REVERT: C 473 TYR cc_start: 0.6721 (t80) cc_final: 0.6463 (t80) REVERT: C 494 SER cc_start: 0.8413 (t) cc_final: 0.8197 (p) REVERT: A 18 LEU cc_start: 0.7661 (mt) cc_final: 0.7196 (mp) REVERT: A 52 LEU cc_start: 0.8718 (tp) cc_final: 0.8489 (tp) REVERT: A 92 THR cc_start: 0.8816 (OUTLIER) cc_final: 0.8475 (p) REVERT: A 96 TYR cc_start: 0.8337 (m-80) cc_final: 0.8113 (m-80) REVERT: B 20 ILE cc_start: 0.7900 (OUTLIER) cc_final: 0.7699 (mm) REVERT: B 55 LYS cc_start: 0.6929 (OUTLIER) cc_final: 0.6544 (mptp) REVERT: B 83 GLU cc_start: 0.7225 (mp0) cc_final: 0.6846 (mp0) outliers start: 20 outliers final: 8 residues processed: 108 average time/residue: 0.5300 time to fit residues: 60.9321 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 : 0.367 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.3980 chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 0.0070 chunk 4 optimal weight: 0.0980 chunk 17 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 35 optimal weight: 0.4980 chunk 10 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 overall best weight: 0.3398 ------------------------------------------------------------------------------- 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: 0.7301 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3389 Z= 0.236 Angle : 0.607 10.271 4619 Z= 0.294 Chirality : 0.044 0.215 516 Planarity : 0.005 0.061 590 Dihedral : 5.559 43.254 477 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 4.10 % Allowed : 17.21 % 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: -2.82 (0.39), residues: 422 helix: -4.99 (0.26), residues: 20 sheet: -0.80 (0.42), residues: 141 loop : -2.35 (0.38), residues: 261 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 0.020 0.001 PHE A 24 TYR 0.015 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 116 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.372 Fit side-chains REVERT: C 341 VAL cc_start: 0.8819 (m) cc_final: 0.8598 (p) REVERT: C 395 VAL cc_start: 0.8811 (OUTLIER) cc_final: 0.8415 (m) REVERT: C 396 TYR cc_start: 0.7613 (m-80) cc_final: 0.7083 (m-80) REVERT: C 407 VAL cc_start: 0.8656 (t) cc_final: 0.8443 (p) REVERT: C 429 PHE cc_start: 0.7613 (t80) cc_final: 0.7405 (t80) REVERT: C 438 SER cc_start: 0.8561 (p) cc_final: 0.8249 (p) REVERT: C 445 VAL cc_start: 0.8536 (t) cc_final: 0.8318 (m) REVERT: C 456 PHE cc_start: 0.7146 (m-80) cc_final: 0.6906 (m-80) REVERT: C 494 SER cc_start: 0.8444 (t) cc_final: 0.8202 (p) REVERT: C 512 VAL cc_start: 0.8120 (m) cc_final: 0.7850 (p) REVERT: A 18 LEU cc_start: 0.7687 (mt) cc_final: 0.7225 (mp) REVERT: A 52 LEU cc_start: 0.8727 (tp) cc_final: 0.8501 (tp) REVERT: A 92 THR cc_start: 0.8817 (OUTLIER) cc_final: 0.8471 (p) REVERT: A 96 TYR cc_start: 0.8333 (m-80) cc_final: 0.8115 (m-80) REVERT: B 20 ILE cc_start: 0.7853 (OUTLIER) cc_final: 0.7641 (mm) REVERT: B 55 LYS cc_start: 0.6952 (OUTLIER) cc_final: 0.6567 (mptp) REVERT: B 63 ARG cc_start: 0.8439 (mtp180) cc_final: 0.8101 (mtp180) REVERT: B 83 GLU cc_start: 0.7303 (mp0) cc_final: 0.6917 (mp0) outliers start: 15 outliers final: 7 residues processed: 111 average time/residue: 0.5119 time to fit residues: 60.5778 Evaluate side-chains 111 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 393 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 20 ILE 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: 0.9990 chunk 16 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 13 optimal weight: 0.0030 chunk 7 optimal weight: 0.3980 overall best weight: 0.4790 ------------------------------------------------------------------------------- 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 40 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 3389 Z= 0.319 Angle : 0.651 11.515 4619 Z= 0.316 Chirality : 0.045 0.208 516 Planarity : 0.005 0.060 590 Dihedral : 5.488 34.721 475 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.95 % Favored : 90.05 % Rotamer: Outliers : 4.37 % Allowed : 18.85 % Favored : 76.78 % 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: -2.72 (0.40), residues: 422 helix: -4.94 (0.28), residues: 20 sheet: -0.72 (0.43), residues: 141 loop : -2.28 (0.38), residues: 261 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 0.032 0.002 PHE C 342 TYR 0.014 0.002 TYR C 453 ARG 0.002 0.000 ARG C 408 *********************** 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 120 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.377 Fit side-chains REVERT: C 395 VAL cc_start: 0.8814 (OUTLIER) cc_final: 0.8425 (m) REVERT: C 396 TYR cc_start: 0.7599 (m-80) cc_final: 0.7090 (m-80) REVERT: C 399 SER cc_start: 0.8501 (m) cc_final: 0.8085 (p) REVERT: C 407 VAL cc_start: 0.8668 (t) cc_final: 0.8446 (p) REVERT: C 429 PHE cc_start: 0.7691 (t80) cc_final: 0.7452 (t80) REVERT: C 438 SER cc_start: 0.8568 (p) cc_final: 0.8292 (p) REVERT: C 445 VAL cc_start: 0.8532 (t) cc_final: 0.8323 (m) REVERT: C 473 TYR cc_start: 0.6600 (t80) cc_final: 0.6163 (t80) REVERT: C 494 SER cc_start: 0.8497 (t) cc_final: 0.8255 (p) REVERT: C 503 VAL cc_start: 0.8451 (t) cc_final: 0.8082 (p) REVERT: C 512 VAL cc_start: 0.8266 (m) cc_final: 0.7932 (p) REVERT: A 52 LEU cc_start: 0.8727 (tp) cc_final: 0.8493 (tp) REVERT: A 92 THR cc_start: 0.8823 (OUTLIER) cc_final: 0.8475 (p) REVERT: A 96 TYR cc_start: 0.8352 (m-80) cc_final: 0.8127 (m-80) REVERT: B 20 ILE cc_start: 0.7876 (OUTLIER) cc_final: 0.7665 (mm) REVERT: B 55 LYS cc_start: 0.7279 (OUTLIER) cc_final: 0.6888 (mptp) REVERT: B 78 SER cc_start: 0.7723 (t) cc_final: 0.7293 (p) REVERT: B 83 GLU cc_start: 0.7486 (mp0) cc_final: 0.6972 (mp0) outliers start: 16 outliers final: 8 residues processed: 116 average time/residue: 0.4905 time to fit residues: 60.8364 Evaluate side-chains 113 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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 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 20 ILE 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: 0.0670 chunk 9 optimal weight: 0.3980 chunk 39 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 13 optimal weight: 0.1980 chunk 20 optimal weight: 0.0070 chunk 38 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 overall best weight: 0.2536 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3389 Z= 0.195 Angle : 0.620 10.464 4619 Z= 0.295 Chirality : 0.043 0.208 516 Planarity : 0.005 0.057 590 Dihedral : 5.367 37.922 475 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 3.83 % Allowed : 20.77 % 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: -2.52 (0.40), residues: 422 helix: -4.88 (0.30), residues: 20 sheet: -0.61 (0.43), residues: 139 loop : -2.10 (0.39), residues: 263 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 0.024 0.002 PHE C 342 TYR 0.014 0.001 TYR B 51 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 114 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.386 Fit side-chains REVERT: C 392 PHE cc_start: 0.8224 (m-80) cc_final: 0.7882 (m-80) REVERT: C 395 VAL cc_start: 0.8790 (OUTLIER) cc_final: 0.8414 (m) REVERT: C 396 TYR cc_start: 0.7629 (m-80) cc_final: 0.7152 (m-80) REVERT: C 399 SER cc_start: 0.8537 (m) cc_final: 0.8253 (p) REVERT: C 407 VAL cc_start: 0.8660 (t) cc_final: 0.8450 (p) REVERT: C 429 PHE cc_start: 0.7662 (t80) cc_final: 0.7415 (t80) REVERT: C 438 SER cc_start: 0.8552 (p) cc_final: 0.8224 (p) REVERT: C 473 TYR cc_start: 0.6564 (t80) cc_final: 0.6149 (t80) REVERT: C 494 SER cc_start: 0.8445 (t) cc_final: 0.8211 (p) REVERT: C 503 VAL cc_start: 0.8380 (t) cc_final: 0.7996 (p) REVERT: C 512 VAL cc_start: 0.8192 (m) cc_final: 0.7866 (p) REVERT: C 523 THR cc_start: 0.7707 (p) cc_final: 0.7394 (t) REVERT: A 52 LEU cc_start: 0.8738 (tp) cc_final: 0.8476 (tp) REVERT: A 92 THR cc_start: 0.8809 (OUTLIER) cc_final: 0.8520 (p) REVERT: A 96 TYR cc_start: 0.8322 (m-80) cc_final: 0.8051 (m-80) REVERT: B 55 LYS cc_start: 0.6979 (OUTLIER) cc_final: 0.6597 (mptp) REVERT: B 63 ARG cc_start: 0.8432 (mtp180) cc_final: 0.7969 (mtp180) REVERT: B 83 GLU cc_start: 0.7385 (mp0) cc_final: 0.6873 (mp0) outliers start: 14 outliers final: 8 residues processed: 109 average time/residue: 0.4890 time to fit residues: 56.9761 Evaluate side-chains 102 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 357 ARG 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 24 optimal weight: 0.2980 chunk 18 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 0.1980 chunk 11 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 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 414 GLN C 506 GLN A 78 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 3389 Z= 0.383 Angle : 0.689 12.682 4619 Z= 0.335 Chirality : 0.046 0.211 516 Planarity : 0.005 0.060 590 Dihedral : 5.691 35.774 475 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.61 % Favored : 88.39 % Rotamer: Outliers : 4.92 % Allowed : 21.04 % 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: -2.36 (0.41), residues: 422 helix: -5.03 (0.31), residues: 12 sheet: -0.61 (0.43), residues: 139 loop : -2.03 (0.39), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 49 HIS 0.001 0.000 HIS B 41 PHE 0.008 0.001 PHE A 107 TYR 0.017 0.002 TYR C 453 ARG 0.002 0.000 ARG C 498 *********************** 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 111 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.360 Fit side-chains REVERT: C 396 TYR cc_start: 0.7616 (m-80) cc_final: 0.7168 (m-80) REVERT: C 399 SER cc_start: 0.8574 (m) cc_final: 0.8201 (p) REVERT: C 429 PHE cc_start: 0.7778 (t80) cc_final: 0.7575 (t80) REVERT: C 438 SER cc_start: 0.8600 (p) cc_final: 0.8333 (p) REVERT: C 473 TYR cc_start: 0.6548 (t80) cc_final: 0.6162 (t80) REVERT: A 52 LEU cc_start: 0.8722 (tp) cc_final: 0.8472 (tp) REVERT: A 92 THR cc_start: 0.8848 (OUTLIER) cc_final: 0.8518 (p) REVERT: B 18 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7948 (pt) REVERT: B 55 LYS cc_start: 0.7298 (OUTLIER) cc_final: 0.6833 (mptp) REVERT: B 83 GLU cc_start: 0.7559 (mp0) cc_final: 0.7032 (mp0) outliers start: 18 outliers final: 11 residues processed: 103 average time/residue: 0.5684 time to fit residues: 62.0329 Evaluate side-chains 101 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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 382 VAL 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 18 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 37 optimal weight: 0.3980 chunk 34 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 16 optimal weight: 0.2980 chunk 28 optimal weight: 0.1980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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: 0.7339 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 3389 Z= 0.316 Angle : 0.676 12.093 4619 Z= 0.325 Chirality : 0.045 0.218 516 Planarity : 0.005 0.058 590 Dihedral : 5.570 33.662 474 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 4.37 % Allowed : 22.13 % Favored : 73.50 % 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: -2.24 (0.41), residues: 422 helix: -4.97 (0.34), residues: 12 sheet: -0.74 (0.41), residues: 152 loop : -1.84 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 436 HIS 0.001 0.000 HIS B 41 PHE 0.016 0.002 PHE A 24 TYR 0.015 0.002 TYR C 453 ARG 0.002 0.000 ARG C 408 *********************** 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 107 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: C 396 TYR cc_start: 0.7623 (m-80) cc_final: 0.7163 (m-80) REVERT: C 399 SER cc_start: 0.8590 (m) cc_final: 0.8194 (p) REVERT: C 438 SER cc_start: 0.8561 (p) cc_final: 0.8252 (p) REVERT: C 473 TYR cc_start: 0.6557 (t80) cc_final: 0.6202 (t80) REVERT: C 523 THR cc_start: 0.7720 (p) cc_final: 0.7364 (t) REVERT: A 52 LEU cc_start: 0.8738 (tp) cc_final: 0.8498 (tp) REVERT: A 92 THR cc_start: 0.8821 (OUTLIER) cc_final: 0.8506 (p) REVERT: B 18 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7922 (pt) REVERT: B 55 LYS cc_start: 0.7102 (OUTLIER) cc_final: 0.6665 (mptp) REVERT: B 83 GLU cc_start: 0.7522 (mp0) cc_final: 0.6990 (mp0) outliers start: 16 outliers final: 7 residues processed: 101 average time/residue: 0.6059 time to fit residues: 64.8091 Evaluate side-chains 98 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 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 18 ILE 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: 0.9990 chunk 33 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 36 optimal weight: 0.1980 chunk 24 optimal weight: 0.0270 chunk 38 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 18 optimal weight: 0.3980 chunk 27 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 overall best weight: 0.3638 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3389 Z= 0.262 Angle : 0.666 12.069 4619 Z= 0.319 Chirality : 0.045 0.198 516 Planarity : 0.005 0.058 590 Dihedral : 5.263 35.998 472 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.95 % Favored : 90.05 % Rotamer: Outliers : 2.73 % Allowed : 24.32 % 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: -2.12 (0.41), residues: 422 helix: -4.92 (0.38), residues: 12 sheet: -0.51 (0.44), residues: 141 loop : -1.83 (0.39), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 436 HIS 0.001 0.000 HIS B 41 PHE 0.008 0.001 PHE A 107 TYR 0.015 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 99 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: C 392 PHE cc_start: 0.8317 (m-80) cc_final: 0.7937 (m-80) REVERT: C 396 TYR cc_start: 0.7660 (m-80) cc_final: 0.7210 (m-80) REVERT: C 399 SER cc_start: 0.8595 (m) cc_final: 0.8212 (p) REVERT: C 438 SER cc_start: 0.8527 (p) cc_final: 0.8230 (p) REVERT: C 473 TYR cc_start: 0.6509 (t80) cc_final: 0.6126 (t80) REVERT: C 523 THR cc_start: 0.7703 (p) cc_final: 0.7359 (t) REVERT: A 52 LEU cc_start: 0.8738 (tp) cc_final: 0.8500 (tp) REVERT: A 92 THR cc_start: 0.8820 (OUTLIER) cc_final: 0.8502 (p) REVERT: B 18 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7909 (pt) REVERT: B 55 LYS cc_start: 0.7047 (OUTLIER) cc_final: 0.6588 (mptp) REVERT: B 83 GLU cc_start: 0.7500 (mp0) cc_final: 0.6975 (mp0) outliers start: 10 outliers final: 6 residues processed: 96 average time/residue: 0.5658 time to fit residues: 57.6895 Evaluate side-chains 97 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 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 18 ILE 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: 0.7980 chunk 3 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 9 optimal weight: 0.2980 chunk 29 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 13 optimal weight: 0.0770 chunk 33 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 overall best weight: 0.4538 ------------------------------------------------------------------------------- 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: 0.7334 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 3389 Z= 0.315 Angle : 0.703 12.587 4619 Z= 0.335 Chirality : 0.045 0.193 516 Planarity : 0.005 0.058 590 Dihedral : 5.429 38.630 472 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % Rotamer: Outliers : 3.01 % Allowed : 24.04 % 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: -2.16 (0.41), residues: 422 helix: -4.92 (0.38), residues: 12 sheet: -0.68 (0.41), residues: 152 loop : -1.78 (0.40), residues: 258 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 0.014 0.002 PHE A 24 TYR 0.016 0.002 TYR C 453 ARG 0.003 0.000 ARG C 408 ********************** 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 104 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.374 Fit side-chains REVERT: C 360 ASN cc_start: 0.8240 (m110) cc_final: 0.7718 (m-40) REVERT: C 396 TYR cc_start: 0.7668 (m-80) cc_final: 0.7219 (m-80) REVERT: C 399 SER cc_start: 0.8591 (m) cc_final: 0.8197 (p) REVERT: C 438 SER cc_start: 0.8546 (p) cc_final: 0.8249 (p) REVERT: C 473 TYR cc_start: 0.6531 (t80) cc_final: 0.6148 (t80) REVERT: C 523 THR cc_start: 0.7685 (p) cc_final: 0.7377 (t) REVERT: A 52 LEU cc_start: 0.8735 (tp) cc_final: 0.8491 (tp) REVERT: A 92 THR cc_start: 0.8835 (OUTLIER) cc_final: 0.8527 (p) REVERT: B 18 ILE cc_start: 0.8153 (OUTLIER) cc_final: 0.7903 (pt) REVERT: B 55 LYS cc_start: 0.7052 (OUTLIER) cc_final: 0.6594 (mptp) REVERT: B 78 SER cc_start: 0.7688 (t) cc_final: 0.7256 (p) REVERT: B 83 GLU cc_start: 0.7523 (mp0) cc_final: 0.6986 (mp0) outliers start: 11 outliers final: 6 residues processed: 99 average time/residue: 0.5542 time to fit residues: 58.1721 Evaluate side-chains 100 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 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 18 ILE 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: 0.9980 chunk 23 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 21 optimal weight: 0.0870 chunk 27 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 16 optimal weight: 0.3980 chunk 15 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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 = 0.3759 r_free = 0.3759 target = 0.130179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.119011 restraints weight = 5115.121| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.28 r_work: 0.3485 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 3389 Z= 0.337 Angle : 0.711 12.647 4619 Z= 0.341 Chirality : 0.046 0.191 516 Planarity : 0.005 0.059 590 Dihedral : 5.493 37.560 472 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.90 % Favored : 89.10 % Rotamer: Outliers : 2.73 % Allowed : 24.59 % 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: -2.11 (0.41), residues: 422 helix: -4.93 (0.37), residues: 12 sheet: -0.63 (0.42), residues: 151 loop : -1.76 (0.40), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 436 HIS 0.001 0.000 HIS B 41 PHE 0.014 0.002 PHE C 400 TYR 0.017 0.002 TYR C 453 ARG 0.003 0.000 ARG C 408 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1904.16 seconds wall clock time: 35 minutes 6.63 seconds (2106.63 seconds total)