Starting phenix.real_space_refine on Wed Mar 5 16:56:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t6b_41068/03_2025/8t6b_41068.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t6b_41068/03_2025/8t6b_41068.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t6b_41068/03_2025/8t6b_41068.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t6b_41068/03_2025/8t6b_41068.map" model { file = "/net/cci-nas-00/data/ceres_data/8t6b_41068/03_2025/8t6b_41068.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t6b_41068/03_2025/8t6b_41068.cif" } resolution = 3.72 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= 0.001 sd= 0.017 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 28 5.16 5 C 1940 2.51 5 N 455 2.21 5 O 493 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2916 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2903 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 23, 'TRANS': 363} Chain breaks: 1 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'SRO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.18, per 1000 atoms: 1.09 Number of scatterers: 2916 At special positions: 0 Unit cell: (76.582, 66.198, 72.688, 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 28 16.00 O 493 8.00 N 455 7.00 C 1940 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: 0.73 Conformation dependent library (CDL) restraints added in 363.7 milliseconds 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 698 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 0 sheets defined 89.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 20 through 35 removed outlier: 3.619A pdb=" N PHE A 24 " --> pdb=" O LYS A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 52 removed outlier: 3.696A pdb=" N VAL A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Proline residue: A 42 - end of helix Proline residue: A 45 - end of helix removed outlier: 3.508A pdb=" N LYS A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 157 removed outlier: 4.388A pdb=" N LEU A 133 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N LYS A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ALA A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Proline residue: A 147 - end of helix Processing helix chain 'A' and resid 158 through 179 removed outlier: 3.560A pdb=" N PHE A 170 " --> pdb=" O PHE A 166 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE A 178 " --> pdb=" O ILE A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 212 removed outlier: 4.014A pdb=" N ALA A 188 " --> pdb=" O PHE A 184 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 221 removed outlier: 5.039A pdb=" N ASN A 219 " --> pdb=" O GLU A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 247 removed outlier: 3.679A pdb=" N MET A 230 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY A 231 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Proline residue: A 236 - end of helix removed outlier: 4.094A pdb=" N LEU A 242 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N TYR A 243 " --> pdb=" O GLY A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 266 removed outlier: 4.658A pdb=" N PHE A 252 " --> pdb=" O LYS A 248 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 269 No H-bonds generated for 'chain 'A' and resid 267 through 269' Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 291 through 322 removed outlier: 3.866A pdb=" N LEU A 295 " --> pdb=" O ASP A 291 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE A 296 " --> pdb=" O PRO A 292 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA A 297 " --> pdb=" O TYR A 293 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER A 300 " --> pdb=" O ILE A 296 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ILE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Proline residue: A 313 - end of helix Proline residue: A 316 - end of helix Processing helix chain 'A' and resid 331 through 333 No H-bonds generated for 'chain 'A' and resid 331 through 333' Processing helix chain 'A' and resid 334 through 352 removed outlier: 3.619A pdb=" N ILE A 343 " --> pdb=" O ILE A 339 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N PHE A 348 " --> pdb=" O GLY A 344 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY A 349 " --> pdb=" O THR A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 355 No H-bonds generated for 'chain 'A' and resid 353 through 355' Processing helix chain 'A' and resid 356 through 372 removed outlier: 3.918A pdb=" N LEU A 363 " --> pdb=" O LEU A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 383 Processing helix chain 'A' and resid 384 through 403 removed outlier: 3.638A pdb=" N GLY A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE A 393 " --> pdb=" O PHE A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 414 removed outlier: 3.679A pdb=" N VAL A 410 " --> pdb=" O MET A 406 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU A 412 " --> pdb=" O TYR A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 447 removed outlier: 3.881A pdb=" N ILE A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA A 425 " --> pdb=" O VAL A 421 " (cutoff:3.500A) Proline residue: A 437 - end of helix removed outlier: 4.016A pdb=" N ALA A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LYS A 445 " --> pdb=" O GLY A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 464 removed outlier: 3.694A pdb=" N ALA A 464 " --> pdb=" O ASP A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 472 removed outlier: 3.864A pdb=" N SER A 472 " --> pdb=" O PHE A 469 " (cutoff:3.500A) 207 hydrogen bonds defined for protein. 606 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: 0.73 Time building geometry restraints manager: 0.87 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: 873 1.35 - 1.46: 702 1.46 - 1.58: 1363 1.58 - 1.70: 0 1.70 - 1.82: 48 Bond restraints: 2986 Sorted by residual: bond pdb=" CG LEU A 409 " pdb=" CD1 LEU A 409 " ideal model delta sigma weight residual 1.521 1.463 0.058 3.30e-02 9.18e+02 3.07e+00 bond pdb=" C ALA A 464 " pdb=" N PRO A 465 " ideal model delta sigma weight residual 1.335 1.354 -0.020 1.19e-02 7.06e+03 2.74e+00 bond pdb=" CA VAL A 41 " pdb=" CB VAL A 41 " ideal model delta sigma weight residual 1.534 1.544 -0.010 6.80e-03 2.16e+04 2.03e+00 bond pdb=" CA VAL A 41 " pdb=" C VAL A 41 " ideal model delta sigma weight residual 1.520 1.531 -0.011 8.80e-03 1.29e+04 1.58e+00 bond pdb=" CA SER A 400 " pdb=" C SER A 400 " ideal model delta sigma weight residual 1.523 1.506 0.017 1.41e-02 5.03e+03 1.41e+00 ... (remaining 2981 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 3917 1.78 - 3.56: 105 3.56 - 5.33: 28 5.33 - 7.11: 6 7.11 - 8.89: 3 Bond angle restraints: 4059 Sorted by residual: angle pdb=" C GLY A 247 " pdb=" N LYS A 248 " pdb=" CA LYS A 248 " ideal model delta sigma weight residual 120.28 124.94 -4.66 1.34e+00 5.57e-01 1.21e+01 angle pdb=" N TYR A 158 " pdb=" CA TYR A 158 " pdb=" C TYR A 158 " ideal model delta sigma weight residual 109.81 116.41 -6.60 2.21e+00 2.05e-01 8.93e+00 angle pdb=" C VAL A 40 " pdb=" N VAL A 41 " pdb=" CA VAL A 41 " ideal model delta sigma weight residual 120.24 122.06 -1.82 6.30e-01 2.52e+00 8.34e+00 angle pdb=" C PHE A 463 " pdb=" N ALA A 464 " pdb=" CA ALA A 464 " ideal model delta sigma weight residual 120.58 124.34 -3.76 1.32e+00 5.74e-01 8.10e+00 angle pdb=" N ILE A 447 " pdb=" CA ILE A 447 " pdb=" C ILE A 447 " ideal model delta sigma weight residual 113.71 111.17 2.54 9.50e-01 1.11e+00 7.14e+00 ... (remaining 4054 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.53: 1531 15.53 - 31.06: 160 31.06 - 46.59: 52 46.59 - 62.12: 6 62.12 - 77.65: 3 Dihedral angle restraints: 1752 sinusoidal: 657 harmonic: 1095 Sorted by residual: dihedral pdb=" CA PHE A 184 " pdb=" C PHE A 184 " pdb=" N LEU A 185 " pdb=" CA LEU A 185 " ideal model delta harmonic sigma weight residual 180.00 157.71 22.29 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA ASN A 34 " pdb=" C ASN A 34 " pdb=" N MET A 35 " pdb=" CA MET A 35 " ideal model delta harmonic sigma weight residual 180.00 159.66 20.34 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA THR A 38 " pdb=" C THR A 38 " pdb=" N VAL A 39 " pdb=" CA VAL A 39 " ideal model delta harmonic sigma weight residual 180.00 161.67 18.33 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 1749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 272 0.028 - 0.057: 127 0.057 - 0.085: 51 0.085 - 0.113: 30 0.113 - 0.142: 3 Chirality restraints: 483 Sorted by residual: chirality pdb=" CA VAL A 417 " pdb=" N VAL A 417 " pdb=" C VAL A 417 " pdb=" CB VAL A 417 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA PRO A 161 " pdb=" N PRO A 161 " pdb=" C PRO A 161 " pdb=" CB PRO A 161 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.75e-01 chirality pdb=" CA VAL A 415 " pdb=" N VAL A 415 " pdb=" C VAL A 415 " pdb=" CB VAL A 415 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.11 2.00e-01 2.50e+01 3.30e-01 ... (remaining 480 not shown) Planarity restraints: 497 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 235 " -0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO A 236 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 236 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 236 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 244 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.11e+00 pdb=" CD GLU A 244 " 0.030 2.00e-02 2.50e+03 pdb=" OE1 GLU A 244 " -0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU A 244 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 312 " -0.027 5.00e-02 4.00e+02 4.05e-02 2.63e+00 pdb=" N PRO A 313 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 313 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 313 " -0.023 5.00e-02 4.00e+02 ... (remaining 494 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 576 2.77 - 3.30: 2987 3.30 - 3.83: 4767 3.83 - 4.37: 5321 4.37 - 4.90: 9352 Nonbonded interactions: 23003 Sorted by model distance: nonbonded pdb=" OH TYR A 293 " pdb=" O PHE A 469 " model vdw 2.237 3.040 nonbonded pdb=" OG1 THR A 212 " pdb=" N ASP A 213 " model vdw 2.434 3.120 nonbonded pdb=" O TYR A 211 " pdb=" OG1 THR A 212 " model vdw 2.475 3.040 nonbonded pdb=" OH TYR A 158 " pdb=" OE2 GLU A 278 " model vdw 2.497 3.040 nonbonded pdb=" O ALA A 333 " pdb=" ND2 ASN A 388 " model vdw 2.499 3.120 ... (remaining 22998 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: 3.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.640 Find NCS groups from input model: 0.020 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6559 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 : 0.004 0.058 2986 Z= 0.239 Angle : 0.785 8.888 4059 Z= 0.419 Chirality : 0.042 0.142 483 Planarity : 0.006 0.045 497 Dihedral : 14.454 77.650 1054 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.00 % Allowed : 16.99 % Favored : 83.01 % 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: -1.30 (0.42), residues: 383 helix: -0.53 (0.29), residues: 309 sheet: None (None), residues: 0 loop : -1.62 (0.71), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 358 HIS 0.001 0.001 HIS A 414 PHE 0.012 0.001 PHE A 27 TYR 0.008 0.001 TYR A 341 ARG 0.004 0.001 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.273 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1200 time to fit residues: 7.6842 Evaluate side-chains 49 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 0.0670 chunk 22 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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 = 0.4269 r_free = 0.4269 target = 0.208208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.185354 restraints weight = 3592.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.188377 restraints weight = 2482.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.190709 restraints weight = 1908.872| |-----------------------------------------------------------------------------| r_work (final): 0.4247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6576 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2986 Z= 0.233 Angle : 0.688 6.702 4059 Z= 0.340 Chirality : 0.043 0.158 483 Planarity : 0.006 0.043 497 Dihedral : 6.516 56.601 409 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.53 % Allowed : 16.67 % Favored : 79.81 % 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: -0.72 (0.43), residues: 383 helix: -0.10 (0.30), residues: 306 sheet: None (None), residues: 0 loop : -1.54 (0.66), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 328 HIS 0.003 0.001 HIS A 414 PHE 0.017 0.001 PHE A 468 TYR 0.016 0.001 TYR A 243 ARG 0.003 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.310 Fit side-chains REVERT: A 365 MET cc_start: 0.5599 (mmm) cc_final: 0.5278 (mmm) outliers start: 11 outliers final: 6 residues processed: 55 average time/residue: 0.1074 time to fit residues: 7.7990 Evaluate side-chains 52 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 415 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 34 optimal weight: 0.3980 chunk 27 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 29 optimal weight: 0.0070 chunk 0 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 chunk 14 optimal weight: 1.9990 overall best weight: 0.4398 ------------------------------------------------------------------------------- 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 = 0.4273 r_free = 0.4273 target = 0.207487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.184571 restraints weight = 3622.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.187157 restraints weight = 2602.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.189707 restraints weight = 2055.556| |-----------------------------------------------------------------------------| r_work (final): 0.4135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6559 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2986 Z= 0.206 Angle : 0.659 6.696 4059 Z= 0.323 Chirality : 0.042 0.150 483 Planarity : 0.006 0.041 497 Dihedral : 5.782 40.857 409 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.49 % Allowed : 17.63 % Favored : 77.88 % 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: -0.41 (0.44), residues: 383 helix: 0.19 (0.31), residues: 302 sheet: None (None), residues: 0 loop : -1.68 (0.67), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 358 HIS 0.001 0.000 HIS A 414 PHE 0.010 0.001 PHE A 27 TYR 0.015 0.001 TYR A 243 ARG 0.005 0.001 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.303 Fit side-chains REVERT: A 148 PHE cc_start: 0.6327 (m-10) cc_final: 0.4759 (t80) REVERT: A 365 MET cc_start: 0.5761 (mmm) cc_final: 0.5233 (mmm) outliers start: 14 outliers final: 6 residues processed: 63 average time/residue: 0.1125 time to fit residues: 9.1565 Evaluate side-chains 55 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 415 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 25 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 15 optimal weight: 0.0030 chunk 7 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 1 optimal weight: 0.0970 chunk 27 optimal weight: 0.0770 chunk 18 optimal weight: 9.9990 chunk 33 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 overall best weight: 0.3146 ------------------------------------------------------------------------------- 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 = 0.4367 r_free = 0.4367 target = 0.216943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.195734 restraints weight = 3733.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.198874 restraints weight = 2626.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.201083 restraints weight = 2044.808| |-----------------------------------------------------------------------------| r_work (final): 0.4262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6516 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2986 Z= 0.183 Angle : 0.682 14.719 4059 Z= 0.320 Chirality : 0.042 0.160 483 Planarity : 0.006 0.038 497 Dihedral : 5.297 29.271 409 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.85 % Allowed : 17.95 % Favored : 78.21 % 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: -0.25 (0.43), residues: 383 helix: 0.33 (0.30), residues: 302 sheet: None (None), residues: 0 loop : -1.72 (0.66), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 358 HIS 0.001 0.000 HIS A 414 PHE 0.009 0.001 PHE A 468 TYR 0.011 0.001 TYR A 243 ARG 0.004 0.001 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.284 Fit side-chains REVERT: A 148 PHE cc_start: 0.6317 (m-10) cc_final: 0.4894 (t80) REVERT: A 365 MET cc_start: 0.5676 (mmm) cc_final: 0.5184 (mmm) REVERT: A 389 PHE cc_start: 0.6138 (OUTLIER) cc_final: 0.5255 (t80) outliers start: 12 outliers final: 5 residues processed: 55 average time/residue: 0.1188 time to fit residues: 8.4052 Evaluate side-chains 48 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 0.0050 chunk 31 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 0.0770 chunk 37 optimal weight: 0.4980 chunk 32 optimal weight: 0.4980 chunk 10 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 overall best weight: 0.3352 ------------------------------------------------------------------------------- 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 = 0.4381 r_free = 0.4381 target = 0.218423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.198069 restraints weight = 3703.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.200631 restraints weight = 2642.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.202865 restraints weight = 2077.800| |-----------------------------------------------------------------------------| r_work (final): 0.4127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6492 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2986 Z= 0.188 Angle : 0.688 11.848 4059 Z= 0.321 Chirality : 0.042 0.156 483 Planarity : 0.006 0.038 497 Dihedral : 5.001 32.981 409 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.81 % Allowed : 16.99 % Favored : 78.21 % 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: -0.09 (0.44), residues: 383 helix: 0.42 (0.30), residues: 303 sheet: None (None), residues: 0 loop : -1.60 (0.68), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 328 HIS 0.001 0.000 HIS A 414 PHE 0.011 0.001 PHE A 393 TYR 0.007 0.001 TYR A 243 ARG 0.003 0.000 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 0.313 Fit side-chains REVERT: A 148 PHE cc_start: 0.6296 (m-10) cc_final: 0.4896 (t80) REVERT: A 365 MET cc_start: 0.5783 (mmm) cc_final: 0.5192 (mmm) REVERT: A 389 PHE cc_start: 0.6123 (OUTLIER) cc_final: 0.5257 (t80) outliers start: 15 outliers final: 6 residues processed: 58 average time/residue: 0.1067 time to fit residues: 8.1808 Evaluate side-chains 50 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 32 optimal weight: 0.0770 chunk 8 optimal weight: 0.7980 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 = 0.4282 r_free = 0.4282 target = 0.208595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.185756 restraints weight = 3837.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.188506 restraints weight = 2763.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.190874 restraints weight = 2171.964| |-----------------------------------------------------------------------------| r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6551 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2986 Z= 0.220 Angle : 0.715 10.110 4059 Z= 0.331 Chirality : 0.043 0.185 483 Planarity : 0.006 0.038 497 Dihedral : 5.119 39.588 409 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.17 % Allowed : 17.95 % Favored : 77.88 % 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 (0.44), residues: 383 helix: 0.33 (0.30), residues: 303 sheet: None (None), residues: 0 loop : -1.62 (0.70), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 328 HIS 0.001 0.000 HIS A 414 PHE 0.010 0.001 PHE A 27 TYR 0.008 0.001 TYR A 243 ARG 0.001 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.307 Fit side-chains REVERT: A 148 PHE cc_start: 0.6309 (m-10) cc_final: 0.4913 (t80) REVERT: A 389 PHE cc_start: 0.6089 (OUTLIER) cc_final: 0.5243 (t80) outliers start: 13 outliers final: 8 residues processed: 59 average time/residue: 0.1049 time to fit residues: 8.1689 Evaluate side-chains 54 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4247 r_free = 0.4247 target = 0.204371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.183500 restraints weight = 3876.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.185023 restraints weight = 3470.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.186722 restraints weight = 2865.291| |-----------------------------------------------------------------------------| r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2986 Z= 0.260 Angle : 0.761 9.070 4059 Z= 0.354 Chirality : 0.045 0.192 483 Planarity : 0.006 0.055 497 Dihedral : 5.520 50.450 409 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 4.81 % Allowed : 19.87 % Favored : 75.32 % 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: -0.37 (0.44), residues: 383 helix: 0.16 (0.30), residues: 306 sheet: None (None), residues: 0 loop : -1.45 (0.74), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 328 HIS 0.002 0.001 HIS A 414 PHE 0.012 0.001 PHE A 468 TYR 0.009 0.001 TYR A 211 ARG 0.002 0.000 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.312 Fit side-chains REVERT: A 148 PHE cc_start: 0.6357 (m-10) cc_final: 0.4963 (t80) REVERT: A 169 MET cc_start: 0.5828 (OUTLIER) cc_final: 0.5109 (mtt) REVERT: A 389 PHE cc_start: 0.6188 (OUTLIER) cc_final: 0.5405 (t80) outliers start: 15 outliers final: 9 residues processed: 56 average time/residue: 0.1228 time to fit residues: 8.8026 Evaluate side-chains 54 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 17 optimal weight: 3.9990 chunk 28 optimal weight: 0.4980 chunk 19 optimal weight: 0.0770 chunk 21 optimal weight: 0.5980 chunk 23 optimal weight: 0.0670 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.4076 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.207229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.184304 restraints weight = 3749.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.187076 restraints weight = 2736.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.188785 restraints weight = 2172.596| |-----------------------------------------------------------------------------| r_work (final): 0.4112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6531 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2986 Z= 0.194 Angle : 0.705 8.443 4059 Z= 0.325 Chirality : 0.042 0.157 483 Planarity : 0.006 0.050 497 Dihedral : 5.339 50.339 409 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.81 % Allowed : 18.91 % Favored : 76.28 % 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: -0.02 (0.44), residues: 383 helix: 0.46 (0.31), residues: 303 sheet: None (None), residues: 0 loop : -1.56 (0.72), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 358 HIS 0.001 0.000 HIS A 414 PHE 0.008 0.001 PHE A 27 TYR 0.006 0.001 TYR A 243 ARG 0.004 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.291 Fit side-chains REVERT: A 148 PHE cc_start: 0.6353 (m-10) cc_final: 0.4926 (t80) REVERT: A 169 MET cc_start: 0.5679 (OUTLIER) cc_final: 0.4948 (mtt) REVERT: A 359 LEU cc_start: 0.6705 (mt) cc_final: 0.6253 (mp) REVERT: A 389 PHE cc_start: 0.6071 (OUTLIER) cc_final: 0.5233 (t80) outliers start: 15 outliers final: 9 residues processed: 58 average time/residue: 0.1201 time to fit residues: 8.9105 Evaluate side-chains 57 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 0.0060 chunk 35 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 0.1980 chunk 5 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.4996 ------------------------------------------------------------------------------- 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 = 0.4294 r_free = 0.4294 target = 0.208289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.186708 restraints weight = 3759.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.187800 restraints weight = 3454.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.190633 restraints weight = 2894.765| |-----------------------------------------------------------------------------| r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6563 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 2986 Z= 0.230 Angle : 0.728 8.246 4059 Z= 0.337 Chirality : 0.043 0.195 483 Planarity : 0.006 0.046 497 Dihedral : 5.380 51.976 409 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.85 % Allowed : 20.19 % Favored : 75.96 % 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: -0.01 (0.44), residues: 383 helix: 0.46 (0.31), residues: 303 sheet: None (None), residues: 0 loop : -1.51 (0.71), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 318 HIS 0.001 0.000 HIS A 414 PHE 0.009 0.001 PHE A 27 TYR 0.016 0.001 TYR A 243 ARG 0.004 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.271 Fit side-chains REVERT: A 148 PHE cc_start: 0.6407 (m-10) cc_final: 0.5013 (t80) REVERT: A 169 MET cc_start: 0.5741 (OUTLIER) cc_final: 0.5083 (mtt) REVERT: A 359 LEU cc_start: 0.6798 (mt) cc_final: 0.6392 (mp) REVERT: A 389 PHE cc_start: 0.6093 (OUTLIER) cc_final: 0.5257 (t80) outliers start: 12 outliers final: 7 residues processed: 55 average time/residue: 0.1092 time to fit residues: 7.8937 Evaluate side-chains 57 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 3.9990 chunk 2 optimal weight: 0.0870 chunk 9 optimal weight: 0.0870 chunk 27 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 28 optimal weight: 0.0050 overall best weight: 0.3150 ------------------------------------------------------------------------------- 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 = 0.4300 r_free = 0.4300 target = 0.209858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.186712 restraints weight = 3787.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.189281 restraints weight = 2756.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.191620 restraints weight = 2204.027| |-----------------------------------------------------------------------------| r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6487 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 2986 Z= 0.202 Angle : 0.711 7.845 4059 Z= 0.329 Chirality : 0.042 0.180 483 Planarity : 0.006 0.043 497 Dihedral : 5.227 51.158 409 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.53 % Allowed : 20.51 % Favored : 75.96 % 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: 0.19 (0.44), residues: 383 helix: 0.62 (0.31), residues: 303 sheet: None (None), residues: 0 loop : -1.53 (0.71), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 358 HIS 0.000 0.000 HIS A 414 PHE 0.008 0.001 PHE A 27 TYR 0.013 0.001 TYR A 243 ARG 0.003 0.000 ARG A 357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.304 Fit side-chains REVERT: A 148 PHE cc_start: 0.6367 (m-10) cc_final: 0.4977 (t80) REVERT: A 169 MET cc_start: 0.5706 (OUTLIER) cc_final: 0.5066 (mtt) REVERT: A 359 LEU cc_start: 0.6738 (mt) cc_final: 0.6285 (mp) REVERT: A 389 PHE cc_start: 0.6111 (OUTLIER) cc_final: 0.5224 (t80) outliers start: 11 outliers final: 6 residues processed: 56 average time/residue: 0.1151 time to fit residues: 8.5827 Evaluate side-chains 53 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 17 optimal weight: 0.0870 chunk 4 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 18 optimal weight: 0.0070 chunk 33 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 overall best weight: 0.4576 ------------------------------------------------------------------------------- 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 = 0.4352 r_free = 0.4352 target = 0.214338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.194369 restraints weight = 3724.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.196637 restraints weight = 2747.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.198624 restraints weight = 2224.774| |-----------------------------------------------------------------------------| r_work (final): 0.4145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6547 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 2986 Z= 0.219 Angle : 0.725 7.839 4059 Z= 0.334 Chirality : 0.043 0.165 483 Planarity : 0.006 0.042 497 Dihedral : 5.327 54.573 409 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.53 % Allowed : 21.47 % Favored : 75.00 % 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: 0.18 (0.44), residues: 383 helix: 0.58 (0.30), residues: 306 sheet: None (None), residues: 0 loop : -1.43 (0.72), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 318 HIS 0.001 0.000 HIS A 414 PHE 0.009 0.001 PHE A 27 TYR 0.011 0.001 TYR A 243 ARG 0.001 0.000 ARG A 326 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1421.54 seconds wall clock time: 25 minutes 13.45 seconds (1513.45 seconds total)