Starting phenix.real_space_refine on Fri Dec 27 08:37:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dep_27394/12_2024/8dep_27394.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dep_27394/12_2024/8dep_27394.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dep_27394/12_2024/8dep_27394.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dep_27394/12_2024/8dep_27394.map" model { file = "/net/cci-nas-00/data/ceres_data/8dep_27394/12_2024/8dep_27394.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dep_27394/12_2024/8dep_27394.cif" } resolution = 3.6 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= 0.002 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: 4 Type Number sf(0) Gaussians S 7 5.16 5 C 2175 2.51 5 N 489 2.21 5 O 552 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 3223 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3062 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 13, 'TRANS': 384} Chain breaks: 1 Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1, 'ARG:plan': 11, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 77 Chain: "A" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 161 Unusual residues: {'AJP': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 422 Unresolved non-hydrogen chiralities: 81 Time building chain proxies: 2.63, per 1000 atoms: 0.82 Number of scatterers: 3223 At special positions: 0 Unit cell: (74.52, 69.12, 79.92, 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 7 16.00 O 552 8.00 N 489 7.00 C 2175 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: 0.96 Conformation dependent library (CDL) restraints added in 354.4 milliseconds 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 752 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 0 sheets defined 87.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 23 through 40 removed outlier: 4.147A pdb=" N HIS A 27 " --> pdb=" O ARG A 23 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU A 28 " --> pdb=" O SER A 24 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N CYS A 33 " --> pdb=" O VAL A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 53 Processing helix chain 'A' and resid 60 through 67 Processing helix chain 'A' and resid 67 through 90 removed outlier: 4.010A pdb=" N VAL A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU A 72 " --> pdb=" O ILE A 68 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N VAL A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) Proline residue: A 82 - end of helix Processing helix chain 'A' and resid 91 through 113 removed outlier: 4.063A pdb=" N VAL A 95 " --> pdb=" O ARG A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 132 removed outlier: 3.620A pdb=" N VAL A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR A 129 " --> pdb=" O PHE A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 144 removed outlier: 3.681A pdb=" N SER A 138 " --> pdb=" O ILE A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 179 removed outlier: 3.922A pdb=" N SER A 168 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL A 169 " --> pdb=" O PHE A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 203 removed outlier: 3.616A pdb=" N ALA A 191 " --> pdb=" O TYR A 187 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N PHE A 202 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 263 removed outlier: 3.714A pdb=" N ARG A 263 " --> pdb=" O GLY A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 296 removed outlier: 4.090A pdb=" N ARG A 268 " --> pdb=" O ARG A 264 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU A 269 " --> pdb=" O PRO A 265 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TRP A 270 " --> pdb=" O GLN A 266 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER A 278 " --> pdb=" O TRP A 274 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA A 279 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N HIS A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ILE A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 327 removed outlier: 3.680A pdb=" N GLY A 325 " --> pdb=" O SER A 321 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE A 326 " --> pdb=" O PHE A 322 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 327 " --> pdb=" O ALA A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 356 removed outlier: 3.548A pdb=" N THR A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 360 No H-bonds generated for 'chain 'A' and resid 358 through 360' Processing helix chain 'A' and resid 361 through 391 removed outlier: 3.710A pdb=" N LEU A 379 " --> pdb=" O SER A 375 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL A 380 " --> pdb=" O TYR A 376 " (cutoff:3.500A) Proline residue: A 381 - end of helix removed outlier: 4.683A pdb=" N SER A 390 " --> pdb=" O GLN A 386 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU A 391 " --> pdb=" O ILE A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 419 removed outlier: 3.965A pdb=" N ALA A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LEU A 398 " --> pdb=" O GLU A 394 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 459 removed outlier: 3.561A pdb=" N VAL A 437 " --> pdb=" O GLN A 433 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG A 456 " --> pdb=" O LEU A 452 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLN A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) 238 hydrogen bonds defined for protein. 714 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: 0.81 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 911 1.35 - 1.46: 916 1.46 - 1.58: 1491 1.58 - 1.69: 4 1.69 - 1.81: 11 Bond restraints: 3333 Sorted by residual: bond pdb=" C23 AJP A 703 " pdb=" C24 AJP A 703 " ideal model delta sigma weight residual 1.522 1.610 -0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" C23 AJP A 702 " pdb=" C24 AJP A 702 " ideal model delta sigma weight residual 1.522 1.609 -0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" C05 AJP A 704 " pdb=" C06 AJP A 704 " ideal model delta sigma weight residual 1.534 1.449 0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" C23 AJP A 701 " pdb=" C24 AJP A 701 " ideal model delta sigma weight residual 1.522 1.607 -0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" C23 AJP A 704 " pdb=" C24 AJP A 704 " ideal model delta sigma weight residual 1.522 1.606 -0.084 2.00e-02 2.50e+03 1.77e+01 ... (remaining 3328 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 4364 1.38 - 2.75: 155 2.75 - 4.13: 64 4.13 - 5.51: 26 5.51 - 6.88: 6 Bond angle restraints: 4615 Sorted by residual: angle pdb=" N LEU A 80 " pdb=" CA LEU A 80 " pdb=" C LEU A 80 " ideal model delta sigma weight residual 111.02 114.67 -3.65 1.22e+00 6.72e-01 8.95e+00 angle pdb=" N ILE A 41 " pdb=" CA ILE A 41 " pdb=" C ILE A 41 " ideal model delta sigma weight residual 106.55 110.75 -4.20 1.45e+00 4.76e-01 8.40e+00 angle pdb=" C ILE A 41 " pdb=" CA ILE A 41 " pdb=" CB ILE A 41 " ideal model delta sigma weight residual 112.68 109.72 2.96 1.14e+00 7.69e-01 6.74e+00 angle pdb=" C07 AJP A 701 " pdb=" C06 AJP A 701 " pdb=" C83 AJP A 701 " ideal model delta sigma weight residual 114.76 107.88 6.88 3.00e+00 1.11e-01 5.26e+00 angle pdb=" N PHE A 202 " pdb=" CA PHE A 202 " pdb=" C PHE A 202 " ideal model delta sigma weight residual 111.82 114.30 -2.48 1.16e+00 7.43e-01 4.59e+00 ... (remaining 4610 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.18: 2153 32.18 - 64.37: 52 64.37 - 96.55: 20 96.55 - 128.73: 13 128.73 - 160.91: 2 Dihedral angle restraints: 2240 sinusoidal: 1069 harmonic: 1171 Sorted by residual: dihedral pdb=" O31 AJP A 702 " pdb=" C30 AJP A 702 " pdb=" C32 AJP A 702 " pdb=" O33 AJP A 702 " ideal model delta sinusoidal sigma weight residual 177.28 -21.81 -160.91 1 3.00e+01 1.11e-03 2.07e+01 dihedral pdb=" C29 AJP A 702 " pdb=" C30 AJP A 702 " pdb=" C32 AJP A 702 " pdb=" O33 AJP A 702 " ideal model delta sinusoidal sigma weight residual -60.96 98.67 -159.63 1 3.00e+01 1.11e-03 2.07e+01 dihedral pdb=" C02 AJP A 703 " pdb=" C85 AJP A 703 " pdb=" O84 AJP A 703 " pdb=" C05 AJP A 703 " ideal model delta sinusoidal sigma weight residual -57.60 62.65 -120.25 1 3.00e+01 1.11e-03 1.60e+01 ... (remaining 2237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 512 0.070 - 0.140: 39 0.140 - 0.210: 15 0.210 - 0.280: 11 0.280 - 0.350: 9 Chirality restraints: 586 Sorted by residual: chirality pdb=" C11 AJP A 702 " pdb=" C10 AJP A 702 " pdb=" C12 AJP A 702 " pdb=" C16 AJP A 702 " both_signs ideal model delta sigma weight residual False 2.20 2.55 -0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" C19 AJP A 702 " pdb=" C18 AJP A 702 " pdb=" C20 AJP A 702 " pdb=" C24 AJP A 702 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" C23 AJP A 703 " pdb=" C22 AJP A 703 " pdb=" C24 AJP A 703 " pdb=" O25 AJP A 703 " both_signs ideal model delta sigma weight residual False -2.50 -2.81 0.31 2.00e-01 2.50e+01 2.33e+00 ... (remaining 583 not shown) Planarity restraints: 521 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 93 " -0.042 5.00e-02 4.00e+02 6.47e-02 6.70e+00 pdb=" N PRO A 94 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 94 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 94 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 81 " -0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO A 82 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 82 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 82 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 42 " 0.024 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO A 43 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 43 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 43 " 0.021 5.00e-02 4.00e+02 ... (remaining 518 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 287 2.74 - 3.28: 3597 3.28 - 3.82: 5361 3.82 - 4.36: 5566 4.36 - 4.90: 9822 Nonbonded interactions: 24633 Sorted by model distance: nonbonded pdb=" O ALA A 135 " pdb=" OG SER A 138 " model vdw 2.197 3.040 nonbonded pdb=" O33 AJP A 701 " pdb=" O77 AJP A 701 " model vdw 2.221 3.040 nonbonded pdb=" O LEU A 124 " pdb=" OG SER A 127 " model vdw 2.350 3.040 nonbonded pdb=" O GLN A 433 " pdb=" OG SER A 436 " model vdw 2.410 3.040 nonbonded pdb=" OE1 GLN A 172 " pdb=" OG1 THR A 176 " model vdw 2.424 3.040 ... (remaining 24628 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 group one per residue 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: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.490 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 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 : 0.008 0.088 3333 Z= 0.472 Angle : 0.764 6.883 4615 Z= 0.347 Chirality : 0.067 0.350 586 Planarity : 0.005 0.065 521 Dihedral : 19.701 160.914 1488 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 0.65 % Allowed : 8.09 % Favored : 91.26 % 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: 3.03 (0.41), residues: 394 helix: 2.57 (0.27), residues: 317 sheet: None (None), residues: 0 loop : -0.49 (0.73), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.002 0.001 HIS A 118 PHE 0.008 0.001 PHE A 326 TYR 0.009 0.001 TYR A 35 ARG 0.001 0.000 ARG A 268 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 118 time to evaluate : 0.300 Fit side-chains REVERT: A 45 GLU cc_start: 0.8175 (tt0) cc_final: 0.7965 (tt0) REVERT: A 75 SER cc_start: 0.9174 (m) cc_final: 0.8962 (t) REVERT: A 287 TYR cc_start: 0.8052 (m-80) cc_final: 0.7788 (m-10) REVERT: A 293 ASN cc_start: 0.8596 (t0) cc_final: 0.8333 (t0) REVERT: A 294 GLU cc_start: 0.7821 (tp30) cc_final: 0.7316 (tp30) REVERT: A 306 ASN cc_start: 0.8570 (m-40) cc_final: 0.8217 (t0) REVERT: A 310 ASP cc_start: 0.9019 (t0) cc_final: 0.8749 (t70) REVERT: A 316 LEU cc_start: 0.8900 (tp) cc_final: 0.8699 (tt) REVERT: A 346 GLN cc_start: 0.8607 (mt0) cc_final: 0.8370 (mt0) REVERT: A 361 SER cc_start: 0.8810 (m) cc_final: 0.8587 (t) REVERT: A 412 THR cc_start: 0.8790 (m) cc_final: 0.8456 (m) outliers start: 2 outliers final: 0 residues processed: 119 average time/residue: 0.1269 time to fit residues: 18.6529 Evaluate side-chains 91 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.5980 chunk 29 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 19 optimal weight: 7.9990 chunk 15 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN A 355 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3333 Z= 0.202 Angle : 0.656 7.359 4615 Z= 0.305 Chirality : 0.039 0.206 586 Planarity : 0.004 0.052 521 Dihedral : 12.690 128.191 892 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 3.24 % Allowed : 19.74 % Favored : 77.02 % 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: 3.65 (0.42), residues: 394 helix: 2.87 (0.27), residues: 327 sheet: None (None), residues: 0 loop : -0.02 (0.87), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.008 0.002 HIS A 355 PHE 0.023 0.001 PHE A 141 TYR 0.018 0.002 TYR A 149 ARG 0.001 0.000 ARG A 148 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.342 Fit side-chains REVERT: A 45 GLU cc_start: 0.8203 (tt0) cc_final: 0.7987 (tt0) REVERT: A 123 GLU cc_start: 0.8301 (mm-30) cc_final: 0.8057 (mm-30) REVERT: A 181 SER cc_start: 0.8920 (m) cc_final: 0.8338 (p) REVERT: A 293 ASN cc_start: 0.8548 (t0) cc_final: 0.8106 (t0) REVERT: A 306 ASN cc_start: 0.8341 (m-40) cc_final: 0.7872 (t0) REVERT: A 310 ASP cc_start: 0.8980 (t0) cc_final: 0.8745 (t70) REVERT: A 316 LEU cc_start: 0.8883 (tp) cc_final: 0.8667 (tt) REVERT: A 346 GLN cc_start: 0.8790 (mt0) cc_final: 0.8290 (mt0) REVERT: A 361 SER cc_start: 0.8809 (m) cc_final: 0.8435 (t) outliers start: 10 outliers final: 8 residues processed: 106 average time/residue: 0.1422 time to fit residues: 18.5752 Evaluate side-chains 96 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 444 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3333 Z= 0.245 Angle : 0.625 6.684 4615 Z= 0.297 Chirality : 0.037 0.147 586 Planarity : 0.004 0.048 521 Dihedral : 10.049 127.176 892 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.56 % Allowed : 25.24 % Favored : 71.20 % 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: 3.53 (0.43), residues: 394 helix: 2.83 (0.28), residues: 323 sheet: None (None), residues: 0 loop : -0.12 (0.86), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 107 HIS 0.003 0.001 HIS A 27 PHE 0.017 0.001 PHE A 141 TYR 0.020 0.002 TYR A 287 ARG 0.006 0.001 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.338 Fit side-chains REVERT: A 45 GLU cc_start: 0.8274 (tt0) cc_final: 0.7991 (tt0) REVERT: A 172 GLN cc_start: 0.8602 (tm-30) cc_final: 0.8243 (tm-30) REVERT: A 181 SER cc_start: 0.8890 (m) cc_final: 0.8323 (p) REVERT: A 277 ASN cc_start: 0.8830 (m-40) cc_final: 0.8556 (m110) REVERT: A 287 TYR cc_start: 0.8183 (m-10) cc_final: 0.7980 (m-10) REVERT: A 293 ASN cc_start: 0.8497 (t0) cc_final: 0.7998 (t0) REVERT: A 294 GLU cc_start: 0.7985 (tp30) cc_final: 0.7175 (tp30) REVERT: A 306 ASN cc_start: 0.8463 (m-40) cc_final: 0.7898 (t0) REVERT: A 310 ASP cc_start: 0.9139 (t0) cc_final: 0.8863 (t70) REVERT: A 346 GLN cc_start: 0.8782 (mt0) cc_final: 0.8311 (mt0) REVERT: A 393 LYS cc_start: 0.8666 (tppt) cc_final: 0.8376 (tptp) REVERT: A 411 LYS cc_start: 0.9034 (ttmt) cc_final: 0.8724 (ttpp) outliers start: 11 outliers final: 6 residues processed: 92 average time/residue: 0.1280 time to fit residues: 14.7762 Evaluate side-chains 86 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 444 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 31 optimal weight: 0.0070 chunk 21 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3333 Z= 0.194 Angle : 0.567 8.703 4615 Z= 0.272 Chirality : 0.035 0.110 586 Planarity : 0.004 0.045 521 Dihedral : 7.815 109.311 892 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 3.88 % Allowed : 26.54 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.40 (0.43), residues: 394 helix: 2.73 (0.28), residues: 325 sheet: None (None), residues: 0 loop : -0.23 (0.84), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.003 0.001 HIS A 27 PHE 0.011 0.001 PHE A 141 TYR 0.018 0.002 TYR A 366 ARG 0.005 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.344 Fit side-chains REVERT: A 45 GLU cc_start: 0.8215 (tt0) cc_final: 0.7950 (tt0) REVERT: A 172 GLN cc_start: 0.8578 (tm-30) cc_final: 0.8353 (tm-30) REVERT: A 181 SER cc_start: 0.8951 (m) cc_final: 0.8405 (p) REVERT: A 277 ASN cc_start: 0.8783 (m-40) cc_final: 0.8516 (m-40) REVERT: A 287 TYR cc_start: 0.8146 (m-10) cc_final: 0.7882 (m-10) REVERT: A 293 ASN cc_start: 0.8421 (t0) cc_final: 0.8185 (t0) REVERT: A 294 GLU cc_start: 0.7863 (tp30) cc_final: 0.7647 (tp30) REVERT: A 306 ASN cc_start: 0.8519 (m-40) cc_final: 0.7950 (t0) REVERT: A 310 ASP cc_start: 0.9111 (t0) cc_final: 0.8821 (t0) REVERT: A 346 GLN cc_start: 0.8768 (mt0) cc_final: 0.8265 (mt0) REVERT: A 393 LYS cc_start: 0.8680 (tppt) cc_final: 0.8380 (tptp) REVERT: A 411 LYS cc_start: 0.8910 (ttmt) cc_final: 0.8613 (ttpp) outliers start: 12 outliers final: 6 residues processed: 96 average time/residue: 0.1158 time to fit residues: 14.2234 Evaluate side-chains 91 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 444 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 0.0970 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 7 optimal weight: 0.0770 chunk 22 optimal weight: 0.9990 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3333 Z= 0.174 Angle : 0.550 7.319 4615 Z= 0.268 Chirality : 0.035 0.186 586 Planarity : 0.004 0.044 521 Dihedral : 5.907 54.893 892 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 3.56 % Allowed : 27.18 % Favored : 69.26 % 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: 3.32 (0.43), residues: 394 helix: 2.71 (0.28), residues: 325 sheet: None (None), residues: 0 loop : -0.47 (0.80), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 107 HIS 0.002 0.001 HIS A 27 PHE 0.011 0.001 PHE A 141 TYR 0.023 0.002 TYR A 366 ARG 0.006 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.356 Fit side-chains REVERT: A 45 GLU cc_start: 0.8215 (tt0) cc_final: 0.7944 (tt0) REVERT: A 181 SER cc_start: 0.9003 (m) cc_final: 0.8415 (p) REVERT: A 277 ASN cc_start: 0.8735 (m-40) cc_final: 0.8481 (m110) REVERT: A 287 TYR cc_start: 0.8156 (m-10) cc_final: 0.7551 (m-10) REVERT: A 293 ASN cc_start: 0.8383 (t0) cc_final: 0.7982 (t0) REVERT: A 294 GLU cc_start: 0.7810 (tp30) cc_final: 0.7509 (tp30) REVERT: A 306 ASN cc_start: 0.8451 (m-40) cc_final: 0.7948 (t0) REVERT: A 310 ASP cc_start: 0.9099 (t0) cc_final: 0.8848 (t0) REVERT: A 313 SER cc_start: 0.9324 (p) cc_final: 0.9034 (p) REVERT: A 393 LYS cc_start: 0.8750 (tppt) cc_final: 0.8490 (tptp) REVERT: A 411 LYS cc_start: 0.8868 (ttmt) cc_final: 0.8516 (tttm) outliers start: 11 outliers final: 6 residues processed: 93 average time/residue: 0.1108 time to fit residues: 13.3116 Evaluate side-chains 90 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 444 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 36 optimal weight: 0.0570 chunk 4 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 0.0970 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3333 Z= 0.169 Angle : 0.525 6.914 4615 Z= 0.258 Chirality : 0.034 0.113 586 Planarity : 0.004 0.044 521 Dihedral : 5.338 54.991 892 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 3.24 % Allowed : 27.18 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.34 (0.43), residues: 394 helix: 2.74 (0.28), residues: 325 sheet: None (None), residues: 0 loop : -0.56 (0.78), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 107 HIS 0.002 0.000 HIS A 27 PHE 0.008 0.001 PHE A 141 TYR 0.022 0.002 TYR A 366 ARG 0.005 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8244 (tt0) cc_final: 0.7972 (tt0) REVERT: A 181 SER cc_start: 0.9012 (m) cc_final: 0.8415 (p) REVERT: A 277 ASN cc_start: 0.8698 (m-40) cc_final: 0.8483 (m110) REVERT: A 287 TYR cc_start: 0.8102 (m-10) cc_final: 0.7845 (m-10) REVERT: A 293 ASN cc_start: 0.8342 (t0) cc_final: 0.8128 (t0) REVERT: A 306 ASN cc_start: 0.8406 (m-40) cc_final: 0.7916 (t0) REVERT: A 310 ASP cc_start: 0.9095 (t0) cc_final: 0.8849 (t0) REVERT: A 313 SER cc_start: 0.9330 (OUTLIER) cc_final: 0.9043 (p) REVERT: A 411 LYS cc_start: 0.8921 (ttmt) cc_final: 0.8549 (tttm) outliers start: 10 outliers final: 7 residues processed: 92 average time/residue: 0.1196 time to fit residues: 14.0723 Evaluate side-chains 96 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 444 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3333 Z= 0.208 Angle : 0.546 7.289 4615 Z= 0.269 Chirality : 0.034 0.115 586 Planarity : 0.004 0.044 521 Dihedral : 5.333 54.519 892 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.91 % Allowed : 27.83 % Favored : 69.26 % 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: 3.20 (0.43), residues: 394 helix: 2.66 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -0.64 (0.77), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 363 HIS 0.002 0.001 HIS A 27 PHE 0.008 0.001 PHE A 59 TYR 0.028 0.002 TYR A 149 ARG 0.006 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.313 Fit side-chains REVERT: A 45 GLU cc_start: 0.8252 (tt0) cc_final: 0.8001 (tt0) REVERT: A 72 LEU cc_start: 0.8580 (tt) cc_final: 0.8342 (tp) REVERT: A 277 ASN cc_start: 0.8652 (m-40) cc_final: 0.8447 (m110) REVERT: A 287 TYR cc_start: 0.8188 (m-10) cc_final: 0.7918 (m-10) REVERT: A 293 ASN cc_start: 0.8272 (t0) cc_final: 0.8026 (t0) REVERT: A 294 GLU cc_start: 0.7913 (tp30) cc_final: 0.7422 (tp30) REVERT: A 306 ASN cc_start: 0.8488 (m-40) cc_final: 0.7989 (t0) REVERT: A 310 ASP cc_start: 0.9112 (t0) cc_final: 0.8848 (t0) REVERT: A 313 SER cc_start: 0.9343 (OUTLIER) cc_final: 0.9056 (p) outliers start: 9 outliers final: 8 residues processed: 88 average time/residue: 0.1162 time to fit residues: 13.1267 Evaluate side-chains 91 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 444 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 36 optimal weight: 0.0040 chunk 32 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 31 optimal weight: 0.4980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3333 Z= 0.170 Angle : 0.530 7.189 4615 Z= 0.262 Chirality : 0.033 0.112 586 Planarity : 0.004 0.044 521 Dihedral : 5.249 54.798 892 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.59 % Allowed : 29.13 % Favored : 68.28 % 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: 3.18 (0.43), residues: 394 helix: 2.69 (0.28), residues: 323 sheet: None (None), residues: 0 loop : -0.82 (0.75), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 363 HIS 0.002 0.000 HIS A 27 PHE 0.006 0.001 PHE A 103 TYR 0.022 0.002 TYR A 366 ARG 0.006 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.337 Fit side-chains REVERT: A 45 GLU cc_start: 0.8224 (tt0) cc_final: 0.7956 (tt0) REVERT: A 72 LEU cc_start: 0.8072 (tt) cc_final: 0.7851 (tp) REVERT: A 141 PHE cc_start: 0.8800 (t80) cc_final: 0.7927 (t80) REVERT: A 277 ASN cc_start: 0.8707 (m-40) cc_final: 0.8453 (m-40) REVERT: A 287 TYR cc_start: 0.7942 (m-10) cc_final: 0.7668 (m-10) REVERT: A 293 ASN cc_start: 0.8327 (t0) cc_final: 0.7927 (t0) REVERT: A 294 GLU cc_start: 0.7894 (tp30) cc_final: 0.7256 (tp30) REVERT: A 306 ASN cc_start: 0.8457 (m-40) cc_final: 0.7961 (t0) REVERT: A 310 ASP cc_start: 0.9091 (t0) cc_final: 0.8841 (t0) REVERT: A 313 SER cc_start: 0.9350 (OUTLIER) cc_final: 0.9066 (p) REVERT: A 393 LYS cc_start: 0.8514 (tppt) cc_final: 0.8179 (tppt) outliers start: 8 outliers final: 7 residues processed: 85 average time/residue: 0.1239 time to fit residues: 13.4390 Evaluate side-chains 88 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 444 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 23 optimal weight: 0.1980 chunk 37 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 3 optimal weight: 0.0050 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3333 Z= 0.159 Angle : 0.545 9.233 4615 Z= 0.264 Chirality : 0.034 0.112 586 Planarity : 0.004 0.044 521 Dihedral : 5.205 54.560 892 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.24 % Allowed : 28.48 % Favored : 68.28 % 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: 3.11 (0.43), residues: 394 helix: 2.64 (0.28), residues: 323 sheet: None (None), residues: 0 loop : -0.82 (0.74), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 363 HIS 0.002 0.000 HIS A 27 PHE 0.006 0.001 PHE A 103 TYR 0.027 0.002 TYR A 366 ARG 0.006 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.355 Fit side-chains REVERT: A 45 GLU cc_start: 0.8212 (tt0) cc_final: 0.7980 (tt0) REVERT: A 141 PHE cc_start: 0.8727 (t80) cc_final: 0.7954 (t80) REVERT: A 277 ASN cc_start: 0.8639 (m-40) cc_final: 0.8405 (m-40) REVERT: A 287 TYR cc_start: 0.7915 (m-10) cc_final: 0.7627 (m-10) REVERT: A 293 ASN cc_start: 0.8275 (t0) cc_final: 0.8030 (t0) REVERT: A 294 GLU cc_start: 0.7949 (tp30) cc_final: 0.7416 (tp30) REVERT: A 306 ASN cc_start: 0.8430 (m-40) cc_final: 0.7941 (t0) REVERT: A 310 ASP cc_start: 0.9083 (t0) cc_final: 0.8843 (t0) REVERT: A 313 SER cc_start: 0.9350 (OUTLIER) cc_final: 0.9066 (p) REVERT: A 336 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7413 (mmtt) REVERT: A 362 ILE cc_start: 0.8361 (tp) cc_final: 0.8040 (tp) REVERT: A 363 TRP cc_start: 0.7516 (m-10) cc_final: 0.7170 (m-10) REVERT: A 366 TYR cc_start: 0.8462 (m-80) cc_final: 0.8157 (m-80) REVERT: A 393 LYS cc_start: 0.8359 (tppt) cc_final: 0.8016 (tppt) outliers start: 10 outliers final: 5 residues processed: 89 average time/residue: 0.1047 time to fit residues: 12.2231 Evaluate side-chains 91 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 444 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 0.6980 chunk 18 optimal weight: 0.4980 chunk 24 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3333 Z= 0.189 Angle : 0.569 7.800 4615 Z= 0.274 Chirality : 0.034 0.114 586 Planarity : 0.004 0.044 521 Dihedral : 5.163 53.977 892 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.59 % Allowed : 29.13 % Favored : 68.28 % 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: 3.11 (0.43), residues: 394 helix: 2.65 (0.28), residues: 322 sheet: None (None), residues: 0 loop : -0.84 (0.72), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 363 HIS 0.002 0.001 HIS A 27 PHE 0.009 0.001 PHE A 141 TYR 0.027 0.002 TYR A 366 ARG 0.006 0.000 ARG A 133 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.340 Fit side-chains REVERT: A 45 GLU cc_start: 0.8225 (tt0) cc_final: 0.8012 (tt0) REVERT: A 72 LEU cc_start: 0.8500 (tt) cc_final: 0.8140 (tp) REVERT: A 141 PHE cc_start: 0.8782 (t80) cc_final: 0.7690 (t80) REVERT: A 277 ASN cc_start: 0.8704 (m-40) cc_final: 0.8457 (m-40) REVERT: A 287 TYR cc_start: 0.8064 (m-10) cc_final: 0.7749 (m-10) REVERT: A 293 ASN cc_start: 0.8284 (t0) cc_final: 0.8025 (t0) REVERT: A 294 GLU cc_start: 0.7987 (tp30) cc_final: 0.7393 (tp30) REVERT: A 306 ASN cc_start: 0.8447 (m-40) cc_final: 0.7959 (t0) REVERT: A 310 ASP cc_start: 0.9115 (t0) cc_final: 0.8844 (t0) REVERT: A 313 SER cc_start: 0.9368 (OUTLIER) cc_final: 0.9081 (p) REVERT: A 366 TYR cc_start: 0.8504 (m-80) cc_final: 0.8175 (m-80) REVERT: A 393 LYS cc_start: 0.8357 (tppt) cc_final: 0.7991 (tppt) outliers start: 8 outliers final: 6 residues processed: 83 average time/residue: 0.0981 time to fit residues: 10.7664 Evaluate side-chains 87 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 444 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.0010 chunk 5 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 chunk 15 optimal weight: 0.2980 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.123388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.109527 restraints weight = 5706.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.113099 restraints weight = 2408.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.115432 restraints weight = 1310.697| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.4389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3333 Z= 0.163 Angle : 0.548 7.324 4615 Z= 0.265 Chirality : 0.033 0.112 586 Planarity : 0.004 0.044 521 Dihedral : 5.129 53.975 892 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.59 % Allowed : 29.13 % Favored : 68.28 % 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: 3.09 (0.42), residues: 394 helix: 2.64 (0.28), residues: 322 sheet: None (None), residues: 0 loop : -0.86 (0.71), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 270 HIS 0.002 0.000 HIS A 27 PHE 0.008 0.001 PHE A 141 TYR 0.025 0.001 TYR A 366 ARG 0.006 0.000 ARG A 133 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1047.68 seconds wall clock time: 19 minutes 52.34 seconds (1192.34 seconds total)