Starting phenix.real_space_refine on Thu Nov 14 09:13:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghb_40039/11_2024/8ghb_40039.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghb_40039/11_2024/8ghb_40039.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghb_40039/11_2024/8ghb_40039.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghb_40039/11_2024/8ghb_40039.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghb_40039/11_2024/8ghb_40039.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghb_40039/11_2024/8ghb_40039.cif" } resolution = 2.76 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= 0.034 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: 5 Type Number sf(0) Gaussians Fe 1 7.16 5 S 34 5.16 5 C 3379 2.51 5 N 920 2.21 5 O 955 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 5289 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 658, 5288 Classifications: {'peptide': 658} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 43, 'TRANS': 614} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.15, per 1000 atoms: 0.78 Number of scatterers: 5289 At special positions: 0 Unit cell: (75.44, 62.32, 107.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 1 26.01 S 34 16.00 O 955 8.00 N 920 7.00 C 3379 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.38 Conformation dependent library (CDL) restraints added in 681.9 milliseconds 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1240 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 5 sheets defined 50.0% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 122 through 139 Processing helix chain 'A' and resid 156 through 160 removed outlier: 3.534A pdb=" N LEU A 160 " --> pdb=" O LYS A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 165 Processing helix chain 'A' and resid 167 through 192 removed outlier: 3.519A pdb=" N TYR A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 206 Processing helix chain 'A' and resid 212 through 222 Processing helix chain 'A' and resid 224 through 235 removed outlier: 4.168A pdb=" N PHE A 232 " --> pdb=" O PHE A 228 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU A 233 " --> pdb=" O SER A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 271 Processing helix chain 'A' and resid 279 through 282 Processing helix chain 'A' and resid 336 through 357 Processing helix chain 'A' and resid 364 through 379 Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 395 through 407 Processing helix chain 'A' and resid 412 through 418 Processing helix chain 'A' and resid 423 through 436 removed outlier: 3.621A pdb=" N ALA A 434 " --> pdb=" O ARG A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 450 Processing helix chain 'A' and resid 458 through 483 Processing helix chain 'A' and resid 485 through 491 Processing helix chain 'A' and resid 492 through 504 Processing helix chain 'A' and resid 521 through 537 Processing helix chain 'A' and resid 537 through 545 Processing helix chain 'A' and resid 545 through 552 removed outlier: 4.513A pdb=" N ASP A 549 " --> pdb=" O GLN A 545 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A 552 " --> pdb=" O LEU A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 557 Processing helix chain 'A' and resid 573 through 581 Processing helix chain 'A' and resid 583 through 597 Processing helix chain 'A' and resid 617 through 643 removed outlier: 3.846A pdb=" N LYS A 621 " --> pdb=" O GLY A 617 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 52 removed outlier: 3.500A pdb=" N GLU A 47 " --> pdb=" O VAL A 8 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ARG A 5 " --> pdb=" O VAL A 83 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL A 83 " --> pdb=" O ARG A 5 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ARG A 7 " --> pdb=" O ILE A 81 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ILE A 81 " --> pdb=" O ARG A 7 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA A 9 " --> pdb=" O ASP A 79 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N PHE A 77 " --> pdb=" O GLY A 11 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N TRP A 13 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ALA A 75 " --> pdb=" O TRP A 13 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N PHE A 77 " --> pdb=" O ARG A 98 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ARG A 98 " --> pdb=" O PHE A 77 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ASP A 79 " --> pdb=" O CYS A 96 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 39 removed outlier: 3.808A pdb=" N LEU A 24 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU A 37 " --> pdb=" O VAL A 22 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 141 through 142 Processing sheet with id=AA4, first strand: chain 'A' and resid 242 through 243 removed outlier: 3.569A pdb=" N VAL A 301 " --> pdb=" O ALA A 276 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU A 300 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ILE A 316 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N MET A 302 " --> pdb=" O MET A 314 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 288 through 289 264 hydrogen bonds defined for protein. 744 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.77 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1689 1.34 - 1.46: 882 1.46 - 1.57: 2806 1.57 - 1.69: 0 1.69 - 1.81: 51 Bond restraints: 5428 Sorted by residual: bond pdb=" CG1 ILE A 357 " pdb=" CD1 ILE A 357 " ideal model delta sigma weight residual 1.513 1.455 0.058 3.90e-02 6.57e+02 2.21e+00 bond pdb=" CB PRO A 555 " pdb=" CG PRO A 555 " ideal model delta sigma weight residual 1.492 1.425 0.067 5.00e-02 4.00e+02 1.81e+00 bond pdb=" C ILE A 390 " pdb=" N PRO A 391 " ideal model delta sigma weight residual 1.337 1.353 -0.016 1.24e-02 6.50e+03 1.66e+00 bond pdb=" CA ILE A 390 " pdb=" C ILE A 390 " ideal model delta sigma weight residual 1.524 1.538 -0.013 1.05e-02 9.07e+03 1.62e+00 bond pdb=" CG GLU A 267 " pdb=" CD GLU A 267 " ideal model delta sigma weight residual 1.516 1.485 0.031 2.50e-02 1.60e+03 1.54e+00 ... (remaining 5423 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 7107 1.97 - 3.95: 228 3.95 - 5.92: 34 5.92 - 7.89: 7 7.89 - 9.87: 2 Bond angle restraints: 7378 Sorted by residual: angle pdb=" N PRO A 443 " pdb=" CA PRO A 443 " pdb=" C PRO A 443 " ideal model delta sigma weight residual 110.70 115.33 -4.63 1.22e+00 6.72e-01 1.44e+01 angle pdb=" CA ILE A 390 " pdb=" C ILE A 390 " pdb=" N PRO A 391 " ideal model delta sigma weight residual 118.88 124.08 -5.20 1.54e+00 4.22e-01 1.14e+01 angle pdb=" CA PRO A 443 " pdb=" C PRO A 443 " pdb=" N PRO A 444 " ideal model delta sigma weight residual 117.93 121.92 -3.99 1.20e+00 6.94e-01 1.11e+01 angle pdb=" CA PRO A 391 " pdb=" N PRO A 391 " pdb=" CD PRO A 391 " ideal model delta sigma weight residual 112.00 107.64 4.36 1.40e+00 5.10e-01 9.70e+00 angle pdb=" CA THR A 327 " pdb=" CB THR A 327 " pdb=" CG2 THR A 327 " ideal model delta sigma weight residual 110.50 115.56 -5.06 1.70e+00 3.46e-01 8.86e+00 ... (remaining 7373 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 2968 17.33 - 34.66: 236 34.66 - 51.99: 37 51.99 - 69.32: 16 69.32 - 86.65: 4 Dihedral angle restraints: 3261 sinusoidal: 1348 harmonic: 1913 Sorted by residual: dihedral pdb=" CA ASP A 335 " pdb=" C ASP A 335 " pdb=" N PRO A 336 " pdb=" CA PRO A 336 " ideal model delta harmonic sigma weight residual 180.00 160.18 19.82 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA THR A 537 " pdb=" C THR A 537 " pdb=" N ALA A 538 " pdb=" CA ALA A 538 " ideal model delta harmonic sigma weight residual -180.00 -161.47 -18.53 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA LEU A 382 " pdb=" C LEU A 382 " pdb=" N HIS A 383 " pdb=" CA HIS A 383 " ideal model delta harmonic sigma weight residual -180.00 -163.63 -16.37 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 3258 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 669 0.067 - 0.133: 117 0.133 - 0.200: 7 0.200 - 0.266: 2 0.266 - 0.333: 1 Chirality restraints: 796 Sorted by residual: chirality pdb=" CB THR A 327 " pdb=" CA THR A 327 " pdb=" OG1 THR A 327 " pdb=" CG2 THR A 327 " both_signs ideal model delta sigma weight residual False 2.55 2.22 0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CB ILE A 390 " pdb=" CA ILE A 390 " pdb=" CG1 ILE A 390 " pdb=" CG2 ILE A 390 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CG LEU A 303 " pdb=" CB LEU A 303 " pdb=" CD1 LEU A 303 " pdb=" CD2 LEU A 303 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 793 not shown) Planarity restraints: 959 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 185 " 0.015 2.00e-02 2.50e+03 2.97e-02 8.82e+00 pdb=" C MET A 185 " -0.051 2.00e-02 2.50e+03 pdb=" O MET A 185 " 0.019 2.00e-02 2.50e+03 pdb=" N ALA A 186 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 335 " 0.045 5.00e-02 4.00e+02 6.76e-02 7.31e+00 pdb=" N PRO A 336 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 336 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 336 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 80 " -0.227 9.50e-02 1.11e+02 1.02e-01 6.76e+00 pdb=" NE ARG A 80 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 80 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG A 80 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 80 " -0.005 2.00e-02 2.50e+03 ... (remaining 956 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 60 2.64 - 3.20: 4469 3.20 - 3.77: 9220 3.77 - 4.33: 12610 4.33 - 4.90: 20277 Nonbonded interactions: 46636 Sorted by model distance: nonbonded pdb=" OXT ILE A 663 " pdb="FE FE2 A 901 " model vdw 2.072 3.000 nonbonded pdb=" NE2 HIS A 360 " pdb="FE FE2 A 901 " model vdw 2.150 3.080 nonbonded pdb=" NE2 HIS A 365 " pdb="FE FE2 A 901 " model vdw 2.222 3.080 nonbonded pdb=" O SER A 594 " pdb=" OG SER A 598 " model vdw 2.289 3.040 nonbonded pdb=" O ILE A 371 " pdb=" OG1 THR A 375 " model vdw 2.302 3.040 ... (remaining 46631 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.200 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.140 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 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:16.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 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 : 0.006 0.067 5428 Z= 0.382 Angle : 0.821 9.866 7378 Z= 0.425 Chirality : 0.052 0.333 796 Planarity : 0.009 0.102 959 Dihedral : 13.616 86.652 2021 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.29), residues: 654 helix: -1.16 (0.25), residues: 291 sheet: 0.65 (0.56), residues: 78 loop : -0.55 (0.33), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 208 HIS 0.014 0.002 HIS A 360 PHE 0.023 0.002 PHE A 94 TYR 0.013 0.002 TYR A 97 ARG 0.020 0.001 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.635 Fit side-chains REVERT: A 5 ARG cc_start: 0.8615 (ttm-80) cc_final: 0.8174 (tpt-90) REVERT: A 32 GLU cc_start: 0.8477 (pt0) cc_final: 0.8234 (pt0) REVERT: A 68 HIS cc_start: 0.7788 (t70) cc_final: 0.7329 (t70) REVERT: A 110 GLU cc_start: 0.7626 (tm-30) cc_final: 0.7204 (tm-30) REVERT: A 435 GLN cc_start: 0.8766 (tt0) cc_final: 0.8428 (mp10) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 1.4233 time to fit residues: 158.1278 Evaluate side-chains 58 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 54 optimal weight: 0.9980 chunk 49 optimal weight: 0.4980 chunk 27 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN A 287 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5428 Z= 0.261 Angle : 0.580 7.118 7378 Z= 0.299 Chirality : 0.042 0.154 796 Planarity : 0.005 0.051 959 Dihedral : 4.461 17.850 715 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.46 % Allowed : 10.37 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.31), residues: 654 helix: 0.42 (0.29), residues: 294 sheet: 0.44 (0.54), residues: 72 loop : -0.06 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 197 HIS 0.011 0.001 HIS A 51 PHE 0.009 0.001 PHE A 278 TYR 0.015 0.002 TYR A 460 ARG 0.005 0.001 ARG A 3 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.594 Fit side-chains REVERT: A 21 ARG cc_start: 0.7269 (tpt90) cc_final: 0.6902 (tpt170) REVERT: A 32 GLU cc_start: 0.8497 (pt0) cc_final: 0.8189 (pt0) REVERT: A 68 HIS cc_start: 0.7858 (t70) cc_final: 0.7595 (t-170) REVERT: A 82 THR cc_start: 0.9197 (p) cc_final: 0.8769 (t) REVERT: A 110 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7588 (tm-30) REVERT: A 133 LYS cc_start: 0.8390 (mttt) cc_final: 0.8033 (mtpp) REVERT: A 159 ASP cc_start: 0.8523 (m-30) cc_final: 0.8069 (m-30) REVERT: A 168 GLU cc_start: 0.8118 (tp30) cc_final: 0.7821 (mm-30) REVERT: A 185 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7953 (mtm) REVERT: A 435 GLN cc_start: 0.8852 (tt0) cc_final: 0.8452 (mp10) REVERT: A 589 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8073 (tt) REVERT: A 603 ASP cc_start: 0.8656 (t0) cc_final: 0.8239 (t0) outliers start: 14 outliers final: 4 residues processed: 72 average time/residue: 1.2469 time to fit residues: 93.9060 Evaluate side-chains 66 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 589 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 32 optimal weight: 1.9990 chunk 18 optimal weight: 0.0570 chunk 49 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5428 Z= 0.236 Angle : 0.549 7.668 7378 Z= 0.276 Chirality : 0.041 0.145 796 Planarity : 0.005 0.049 959 Dihedral : 4.250 14.056 715 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.81 % Allowed : 13.01 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.32), residues: 654 helix: 1.01 (0.30), residues: 293 sheet: 0.42 (0.55), residues: 72 loop : 0.17 (0.37), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 176 HIS 0.010 0.001 HIS A 51 PHE 0.011 0.001 PHE A 482 TYR 0.014 0.002 TYR A 460 ARG 0.005 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.606 Fit side-chains REVERT: A 32 GLU cc_start: 0.8513 (pt0) cc_final: 0.8214 (pt0) REVERT: A 68 HIS cc_start: 0.7844 (t70) cc_final: 0.7601 (t-170) REVERT: A 110 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7638 (tm-30) REVERT: A 133 LYS cc_start: 0.8367 (mttt) cc_final: 0.7930 (tppt) REVERT: A 159 ASP cc_start: 0.8486 (m-30) cc_final: 0.8109 (m-30) REVERT: A 168 GLU cc_start: 0.8081 (tp30) cc_final: 0.7825 (mm-30) REVERT: A 219 ARG cc_start: 0.7976 (tmt-80) cc_final: 0.7264 (tpt90) REVERT: A 435 GLN cc_start: 0.8853 (tt0) cc_final: 0.8455 (mp10) REVERT: A 589 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8048 (tt) REVERT: A 603 ASP cc_start: 0.8671 (t0) cc_final: 0.8192 (t0) outliers start: 16 outliers final: 3 residues processed: 75 average time/residue: 1.3210 time to fit residues: 103.3866 Evaluate side-chains 67 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 589 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 58 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 30 optimal weight: 0.0470 chunk 6 optimal weight: 3.9990 chunk 28 optimal weight: 0.0050 chunk 39 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 56 optimal weight: 0.0070 chunk 16 optimal weight: 0.7980 overall best weight: 0.3110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 GLN A 287 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5428 Z= 0.174 Angle : 0.524 7.071 7378 Z= 0.263 Chirality : 0.039 0.142 796 Planarity : 0.004 0.049 959 Dihedral : 4.127 13.702 715 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.34 % Allowed : 12.83 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.32), residues: 654 helix: 1.28 (0.30), residues: 294 sheet: 0.28 (0.55), residues: 72 loop : 0.23 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 70 HIS 0.009 0.001 HIS A 51 PHE 0.009 0.001 PHE A 482 TYR 0.013 0.001 TYR A 460 ARG 0.007 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.657 Fit side-chains REVERT: A 21 ARG cc_start: 0.7129 (tmt170) cc_final: 0.6857 (tpt170) REVERT: A 32 GLU cc_start: 0.8508 (pt0) cc_final: 0.8198 (pt0) REVERT: A 133 LYS cc_start: 0.8353 (mttt) cc_final: 0.7927 (tppt) REVERT: A 156 ARG cc_start: 0.8041 (ttp-110) cc_final: 0.7588 (ptm-80) REVERT: A 159 ASP cc_start: 0.8448 (m-30) cc_final: 0.8132 (m-30) REVERT: A 219 ARG cc_start: 0.7983 (tmt-80) cc_final: 0.7296 (tpt90) REVERT: A 414 PHE cc_start: 0.8339 (OUTLIER) cc_final: 0.8056 (m-80) REVERT: A 435 GLN cc_start: 0.8879 (tt0) cc_final: 0.8455 (mp10) REVERT: A 589 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8091 (tt) REVERT: A 603 ASP cc_start: 0.8689 (t0) cc_final: 0.8149 (t0) outliers start: 19 outliers final: 5 residues processed: 78 average time/residue: 1.2503 time to fit residues: 102.1375 Evaluate side-chains 64 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 589 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 52 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 25 optimal weight: 0.0870 chunk 53 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 56 optimal weight: 0.0470 chunk 15 optimal weight: 0.0970 chunk 21 optimal weight: 0.7980 overall best weight: 0.3654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 GLN A 287 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5428 Z= 0.178 Angle : 0.533 8.153 7378 Z= 0.267 Chirality : 0.040 0.232 796 Planarity : 0.004 0.048 959 Dihedral : 4.030 13.716 715 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.16 % Allowed : 14.59 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.33), residues: 654 helix: 1.43 (0.30), residues: 294 sheet: 0.33 (0.57), residues: 74 loop : 0.30 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 176 HIS 0.012 0.001 HIS A 51 PHE 0.010 0.001 PHE A 278 TYR 0.013 0.001 TYR A 460 ARG 0.005 0.000 ARG A 485 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.667 Fit side-chains REVERT: A 30 ARG cc_start: 0.8053 (ptp-170) cc_final: 0.7752 (ptt-90) REVERT: A 32 GLU cc_start: 0.8505 (pt0) cc_final: 0.8189 (pt0) REVERT: A 110 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7381 (tm-30) REVERT: A 133 LYS cc_start: 0.8353 (mttt) cc_final: 0.7930 (tppt) REVERT: A 146 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7548 (mp0) REVERT: A 156 ARG cc_start: 0.8012 (ttp-110) cc_final: 0.7555 (ptm-80) REVERT: A 159 ASP cc_start: 0.8446 (m-30) cc_final: 0.8135 (m-30) REVERT: A 168 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7941 (tp30) REVERT: A 219 ARG cc_start: 0.7988 (tmt-80) cc_final: 0.7280 (tpt90) REVERT: A 414 PHE cc_start: 0.8377 (OUTLIER) cc_final: 0.8069 (m-80) REVERT: A 435 GLN cc_start: 0.8883 (tt0) cc_final: 0.8453 (mp10) REVERT: A 589 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8111 (tt) REVERT: A 603 ASP cc_start: 0.8677 (t0) cc_final: 0.8073 (t0) outliers start: 18 outliers final: 4 residues processed: 75 average time/residue: 1.2871 time to fit residues: 101.1012 Evaluate side-chains 67 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 593 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 56 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS A 231 GLN A 287 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5428 Z= 0.247 Angle : 0.549 8.396 7378 Z= 0.273 Chirality : 0.041 0.190 796 Planarity : 0.004 0.045 959 Dihedral : 4.012 14.575 715 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.87 % Allowed : 15.47 % Favored : 80.67 % 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: 1.12 (0.32), residues: 654 helix: 1.42 (0.30), residues: 294 sheet: 0.32 (0.56), residues: 74 loop : 0.29 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 176 HIS 0.010 0.001 HIS A 51 PHE 0.012 0.001 PHE A 278 TYR 0.014 0.002 TYR A 460 ARG 0.005 0.000 ARG A 485 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 68 time to evaluate : 0.616 Fit side-chains REVERT: A 32 GLU cc_start: 0.8527 (pt0) cc_final: 0.8219 (pt0) REVERT: A 98 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.8050 (ptp-110) REVERT: A 110 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7412 (tm-30) REVERT: A 133 LYS cc_start: 0.8373 (mttt) cc_final: 0.7944 (tppt) REVERT: A 146 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7549 (mp0) REVERT: A 156 ARG cc_start: 0.8033 (ttp-110) cc_final: 0.7418 (ptm-80) REVERT: A 159 ASP cc_start: 0.8463 (m-30) cc_final: 0.8080 (m-30) REVERT: A 168 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7791 (tp30) REVERT: A 219 ARG cc_start: 0.8048 (tmt-80) cc_final: 0.7311 (tpt90) REVERT: A 435 GLN cc_start: 0.8899 (tt0) cc_final: 0.8426 (mp10) REVERT: A 589 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8109 (tt) REVERT: A 603 ASP cc_start: 0.8699 (t0) cc_final: 0.8091 (t0) outliers start: 22 outliers final: 4 residues processed: 82 average time/residue: 1.2997 time to fit residues: 111.7800 Evaluate side-chains 67 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 593 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 7 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 chunk 37 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS A 231 GLN A 287 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5428 Z= 0.238 Angle : 0.565 8.665 7378 Z= 0.279 Chirality : 0.041 0.179 796 Planarity : 0.004 0.046 959 Dihedral : 4.007 14.125 715 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.81 % Allowed : 17.05 % Favored : 80.14 % 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: 1.12 (0.32), residues: 654 helix: 1.42 (0.30), residues: 294 sheet: 0.22 (0.54), residues: 71 loop : 0.31 (0.37), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 176 HIS 0.010 0.001 HIS A 51 PHE 0.011 0.001 PHE A 278 TYR 0.014 0.001 TYR A 460 ARG 0.007 0.000 ARG A 485 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.682 Fit side-chains REVERT: A 30 ARG cc_start: 0.8184 (ptp-170) cc_final: 0.7890 (ptt-90) REVERT: A 32 GLU cc_start: 0.8520 (pt0) cc_final: 0.8205 (pt0) REVERT: A 98 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.8034 (ptp-110) REVERT: A 110 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7403 (tm-30) REVERT: A 146 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7561 (mp0) REVERT: A 156 ARG cc_start: 0.7997 (ttp-110) cc_final: 0.7379 (ptm-80) REVERT: A 159 ASP cc_start: 0.8467 (m-30) cc_final: 0.8075 (m-30) REVERT: A 219 ARG cc_start: 0.8044 (tmt-80) cc_final: 0.7407 (tpt90) REVERT: A 267 GLU cc_start: 0.7375 (pt0) cc_final: 0.7123 (pt0) REVERT: A 435 GLN cc_start: 0.8892 (tt0) cc_final: 0.8410 (mp10) REVERT: A 589 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8118 (tt) REVERT: A 603 ASP cc_start: 0.8692 (t0) cc_final: 0.8093 (t0) outliers start: 16 outliers final: 5 residues processed: 73 average time/residue: 1.2764 time to fit residues: 97.7028 Evaluate side-chains 65 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 593 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 12 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 30 optimal weight: 0.2980 chunk 5 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 GLN A 287 ASN A 556 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 5428 Z= 0.408 Angle : 0.649 8.562 7378 Z= 0.322 Chirality : 0.044 0.176 796 Planarity : 0.005 0.044 959 Dihedral : 4.212 15.757 715 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.87 % Allowed : 16.70 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.32), residues: 654 helix: 1.22 (0.30), residues: 295 sheet: 0.19 (0.54), residues: 71 loop : 0.28 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 197 HIS 0.010 0.001 HIS A 51 PHE 0.018 0.002 PHE A 278 TYR 0.015 0.002 TYR A 460 ARG 0.008 0.001 ARG A 485 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 62 time to evaluate : 0.641 Fit side-chains REVERT: A 32 GLU cc_start: 0.8538 (pt0) cc_final: 0.8223 (pt0) REVERT: A 98 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.8002 (ptp-110) REVERT: A 110 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7579 (tm-30) REVERT: A 146 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7706 (mp0) REVERT: A 156 ARG cc_start: 0.7997 (ttp-110) cc_final: 0.7368 (ptm-80) REVERT: A 159 ASP cc_start: 0.8498 (m-30) cc_final: 0.8047 (m-30) REVERT: A 485 ARG cc_start: 0.8266 (mtp85) cc_final: 0.7747 (mtp85) REVERT: A 589 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8152 (tt) REVERT: A 603 ASP cc_start: 0.8733 (t0) cc_final: 0.8152 (t0) outliers start: 22 outliers final: 6 residues processed: 77 average time/residue: 1.3084 time to fit residues: 105.3403 Evaluate side-chains 68 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 593 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 25 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 GLN A 287 ASN A 360 HIS A 544 ASN A 556 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5428 Z= 0.255 Angle : 0.602 8.672 7378 Z= 0.300 Chirality : 0.042 0.177 796 Planarity : 0.004 0.044 959 Dihedral : 4.181 15.376 715 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.81 % Allowed : 17.93 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.32), residues: 654 helix: 1.27 (0.30), residues: 295 sheet: 0.12 (0.53), residues: 71 loop : 0.30 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 176 HIS 0.010 0.001 HIS A 51 PHE 0.011 0.001 PHE A 482 TYR 0.014 0.002 TYR A 460 ARG 0.007 0.001 ARG A 485 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.585 Fit side-chains REVERT: A 30 ARG cc_start: 0.8272 (ptp-170) cc_final: 0.7919 (ptt-90) REVERT: A 32 GLU cc_start: 0.8521 (pt0) cc_final: 0.8212 (pt0) REVERT: A 98 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7979 (ptp-110) REVERT: A 110 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7449 (tm-30) REVERT: A 146 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7596 (mp0) REVERT: A 156 ARG cc_start: 0.7953 (ttp-110) cc_final: 0.7347 (ptm-80) REVERT: A 159 ASP cc_start: 0.8510 (m-30) cc_final: 0.8070 (m-30) REVERT: A 185 MET cc_start: 0.8236 (mpp) cc_final: 0.7948 (mmt) REVERT: A 414 PHE cc_start: 0.8523 (OUTLIER) cc_final: 0.8130 (m-80) REVERT: A 435 GLN cc_start: 0.9036 (tt0) cc_final: 0.8410 (mp10) REVERT: A 589 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8012 (tt) REVERT: A 603 ASP cc_start: 0.8705 (t0) cc_final: 0.8112 (t0) outliers start: 16 outliers final: 6 residues processed: 71 average time/residue: 1.1343 time to fit residues: 84.8813 Evaluate side-chains 68 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 593 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 64 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 GLN A 547 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5428 Z= 0.255 Angle : 0.610 9.415 7378 Z= 0.299 Chirality : 0.041 0.180 796 Planarity : 0.004 0.044 959 Dihedral : 4.155 15.406 715 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.46 % Allowed : 18.45 % Favored : 79.09 % 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: 1.03 (0.32), residues: 654 helix: 1.32 (0.30), residues: 295 sheet: 0.09 (0.53), residues: 71 loop : 0.32 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 176 HIS 0.009 0.001 HIS A 51 PHE 0.011 0.001 PHE A 278 TYR 0.014 0.002 TYR A 460 ARG 0.009 0.001 ARG A 485 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.557 Fit side-chains REVERT: A 32 GLU cc_start: 0.8508 (pt0) cc_final: 0.8191 (pt0) REVERT: A 98 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7971 (ptp-110) REVERT: A 110 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7441 (tm-30) REVERT: A 146 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7580 (mp0) REVERT: A 156 ARG cc_start: 0.7963 (ttp-110) cc_final: 0.7385 (ptm-80) REVERT: A 159 ASP cc_start: 0.8517 (m-30) cc_final: 0.8055 (m-30) REVERT: A 185 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7914 (mmt) REVERT: A 287 ASN cc_start: 0.8556 (t0) cc_final: 0.8225 (t0) REVERT: A 414 PHE cc_start: 0.8492 (OUTLIER) cc_final: 0.8197 (m-80) REVERT: A 435 GLN cc_start: 0.9037 (tt0) cc_final: 0.8413 (mp10) REVERT: A 485 ARG cc_start: 0.8277 (mtp85) cc_final: 0.7801 (mtp85) REVERT: A 589 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8013 (tt) REVERT: A 603 ASP cc_start: 0.8705 (t0) cc_final: 0.8117 (t0) outliers start: 14 outliers final: 6 residues processed: 71 average time/residue: 1.2384 time to fit residues: 92.1803 Evaluate side-chains 72 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 597 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 14 optimal weight: 0.3980 chunk 51 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.096978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.082058 restraints weight = 9405.625| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.68 r_work: 0.3019 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5428 Z= 0.253 Angle : 0.610 9.380 7378 Z= 0.299 Chirality : 0.041 0.174 796 Planarity : 0.004 0.045 959 Dihedral : 4.142 15.053 715 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.34 % Allowed : 17.40 % Favored : 79.26 % 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: 1.05 (0.32), residues: 654 helix: 1.34 (0.30), residues: 295 sheet: 0.11 (0.54), residues: 71 loop : 0.32 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 176 HIS 0.010 0.001 HIS A 51 PHE 0.012 0.001 PHE A 278 TYR 0.014 0.002 TYR A 460 ARG 0.009 0.001 ARG A 485 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2426.50 seconds wall clock time: 44 minutes 16.61 seconds (2656.61 seconds total)