Starting phenix.real_space_refine on Wed Mar 5 18:07:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dwi_27755/03_2025/8dwi_27755.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dwi_27755/03_2025/8dwi_27755.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dwi_27755/03_2025/8dwi_27755.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dwi_27755/03_2025/8dwi_27755.map" model { file = "/net/cci-nas-00/data/ceres_data/8dwi_27755/03_2025/8dwi_27755.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dwi_27755/03_2025/8dwi_27755.cif" } resolution = 3.4 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= 0.018 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 14 5.16 5 C 2138 2.51 5 N 504 2.21 5 O 536 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 3192 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3192 Classifications: {'peptide': 424} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 19, 'TRANS': 404} Chain breaks: 1 Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 4, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 71 Time building chain proxies: 2.39, per 1000 atoms: 0.75 Number of scatterers: 3192 At special positions: 0 Unit cell: (71.38, 70.55, 72.21, 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 14 16.00 O 536 8.00 N 504 7.00 C 2138 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: 0.68 Conformation dependent library (CDL) restraints added in 325.2 milliseconds 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 772 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 76.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 38 through 67 removed outlier: 4.163A pdb=" N PHE A 47 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE A 48 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N TYR A 54 " --> pdb=" O PHE A 51 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ASN A 59 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU A 60 " --> pdb=" O ARG A 57 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER A 61 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU A 64 " --> pdb=" O SER A 61 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET A 67 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 133 removed outlier: 4.773A pdb=" N PHE A 115 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N PHE A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR A 117 " --> pdb=" O GLY A 113 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE A 121 " --> pdb=" O TYR A 117 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ILE A 124 " --> pdb=" O ILE A 120 " (cutoff:3.500A) Proline residue: A 125 - end of helix removed outlier: 4.502A pdb=" N TYR A 128 " --> pdb=" O ILE A 124 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS A 132 " --> pdb=" O TYR A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 151 Processing helix chain 'A' and resid 153 through 159 Processing helix chain 'A' and resid 161 through 168 Processing helix chain 'A' and resid 176 through 189 Proline residue: A 180 - end of helix removed outlier: 3.910A pdb=" N SER A 188 " --> pdb=" O ALA A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 223 removed outlier: 3.849A pdb=" N GLY A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ALA A 206 " --> pdb=" O SER A 202 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLN A 207 " --> pdb=" O TYR A 203 " (cutoff:3.500A) Proline residue: A 215 - end of helix Processing helix chain 'A' and resid 226 through 247 removed outlier: 5.193A pdb=" N PHE A 233 " --> pdb=" O PHE A 230 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N TRP A 244 " --> pdb=" O PHE A 241 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ILE A 245 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 289 through 310 Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 324 through 354 removed outlier: 3.981A pdb=" N SER A 331 " --> pdb=" O ASN A 327 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER A 332 " --> pdb=" O GLY A 328 " (cutoff:3.500A) Proline residue: A 334 - end of helix removed outlier: 3.871A pdb=" N GLN A 347 " --> pdb=" O ILE A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 382 removed outlier: 4.217A pdb=" N GLY A 374 " --> pdb=" O ILE A 370 " (cutoff:3.500A) Proline residue: A 375 - end of helix Processing helix chain 'A' and resid 389 through 408 removed outlier: 3.960A pdb=" N PHE A 405 " --> pdb=" O THR A 401 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N CYS A 406 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N SER A 407 " --> pdb=" O GLY A 403 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N SER A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 417 removed outlier: 4.321A pdb=" N LEU A 415 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE A 417 " --> pdb=" O HIS A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 431 Processing helix chain 'A' and resid 435 through 445 Proline residue: A 441 - end of helix Processing helix chain 'A' and resid 453 through 477 Processing helix chain 'A' and resid 484 through 486 No H-bonds generated for 'chain 'A' and resid 484 through 486' 197 hydrogen bonds defined for protein. 480 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: 0.65 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 938 1.34 - 1.46: 817 1.46 - 1.58: 1515 1.58 - 1.69: 0 1.69 - 1.81: 22 Bond restraints: 3292 Sorted by residual: bond pdb=" N TYR A 117 " pdb=" CA TYR A 117 " ideal model delta sigma weight residual 1.457 1.483 -0.025 1.29e-02 6.01e+03 3.89e+00 bond pdb=" N PHE A 115 " pdb=" CA PHE A 115 " ideal model delta sigma weight residual 1.458 1.481 -0.024 1.30e-02 5.92e+03 3.31e+00 bond pdb=" C VAL A 58 " pdb=" O VAL A 58 " ideal model delta sigma weight residual 1.242 1.230 0.012 1.13e-02 7.83e+03 1.22e+00 bond pdb=" C LEU A 214 " pdb=" N PRO A 215 " ideal model delta sigma weight residual 1.335 1.350 -0.015 1.36e-02 5.41e+03 1.18e+00 bond pdb=" C PHE A 115 " pdb=" N PHE A 116 " ideal model delta sigma weight residual 1.334 1.320 0.014 1.43e-02 4.89e+03 9.67e-01 ... (remaining 3287 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 4313 1.28 - 2.56: 148 2.56 - 3.84: 28 3.84 - 5.12: 13 5.12 - 6.40: 5 Bond angle restraints: 4507 Sorted by residual: angle pdb=" N ILE A 435 " pdb=" CA ILE A 435 " pdb=" C ILE A 435 " ideal model delta sigma weight residual 112.61 107.45 5.16 1.45e+00 4.76e-01 1.27e+01 angle pdb=" N PHE A 115 " pdb=" CA PHE A 115 " pdb=" C PHE A 115 " ideal model delta sigma weight residual 112.38 108.50 3.88 1.22e+00 6.72e-01 1.01e+01 angle pdb=" C LYS A 256 " pdb=" N ARG A 257 " pdb=" CA ARG A 257 " ideal model delta sigma weight residual 121.54 127.49 -5.95 1.91e+00 2.74e-01 9.71e+00 angle pdb=" N PHE A 116 " pdb=" CA PHE A 116 " pdb=" C PHE A 116 " ideal model delta sigma weight residual 111.69 107.87 3.82 1.23e+00 6.61e-01 9.63e+00 angle pdb=" N VAL A 177 " pdb=" CA VAL A 177 " pdb=" C VAL A 177 " ideal model delta sigma weight residual 113.07 109.28 3.79 1.36e+00 5.41e-01 7.75e+00 ... (remaining 4502 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.49: 1648 15.49 - 30.97: 142 30.97 - 46.46: 43 46.46 - 61.95: 3 61.95 - 77.44: 2 Dihedral angle restraints: 1838 sinusoidal: 627 harmonic: 1211 Sorted by residual: dihedral pdb=" CA LEU A 170 " pdb=" C LEU A 170 " pdb=" N GLU A 171 " pdb=" CA GLU A 171 " ideal model delta harmonic sigma weight residual 180.00 160.10 19.90 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA LYS A 445 " pdb=" C LYS A 445 " pdb=" N SER A 446 " pdb=" CA SER A 446 " ideal model delta harmonic sigma weight residual 180.00 162.07 17.93 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA ALA A 382 " pdb=" C ALA A 382 " pdb=" N GLY A 383 " pdb=" CA GLY A 383 " ideal model delta harmonic sigma weight residual 180.00 162.09 17.91 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 1835 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 278 0.027 - 0.054: 148 0.054 - 0.082: 58 0.082 - 0.109: 32 0.109 - 0.136: 5 Chirality restraints: 521 Sorted by residual: chirality pdb=" CB VAL A 177 " pdb=" CA VAL A 177 " pdb=" CG1 VAL A 177 " pdb=" CG2 VAL A 177 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.62e-01 chirality pdb=" CA PHE A 115 " pdb=" N PHE A 115 " pdb=" C PHE A 115 " pdb=" CB PHE A 115 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.13 2.00e-01 2.50e+01 4.24e-01 chirality pdb=" CA TRP A 186 " pdb=" N TRP A 186 " pdb=" C TRP A 186 " pdb=" CB TRP A 186 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.70e-01 ... (remaining 518 not shown) Planarity restraints: 547 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 435 " 0.050 5.00e-02 4.00e+02 7.51e-02 9.02e+00 pdb=" N PRO A 436 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 436 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 436 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 162 " -0.041 5.00e-02 4.00e+02 6.20e-02 6.15e+00 pdb=" N PRO A 163 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 163 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 163 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 374 " -0.037 5.00e-02 4.00e+02 5.66e-02 5.13e+00 pdb=" N PRO A 375 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 375 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 375 " -0.032 5.00e-02 4.00e+02 ... (remaining 544 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 816 2.79 - 3.32: 3337 3.32 - 3.84: 5401 3.84 - 4.37: 6043 4.37 - 4.90: 10257 Nonbonded interactions: 25854 Sorted by model distance: nonbonded pdb=" OG1 THR A 304 " pdb=" OD1 ASN A 467 " model vdw 2.258 3.040 nonbonded pdb=" N ASP A 104 " pdb=" OD1 ASP A 104 " model vdw 2.447 3.120 nonbonded pdb=" O ALA A 46 " pdb=" N PHE A 50 " model vdw 2.517 3.120 nonbonded pdb=" O PHE A 116 " pdb=" N GLY A 118 " model vdw 2.524 3.120 nonbonded pdb=" O ASN A 323 " pdb=" N ASN A 327 " model vdw 2.545 3.120 ... (remaining 25849 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.930 Find NCS groups from input model: 0.030 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3203 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 : 0.003 0.032 3292 Z= 0.208 Angle : 0.629 6.398 4507 Z= 0.365 Chirality : 0.042 0.136 521 Planarity : 0.006 0.075 547 Dihedral : 13.015 77.435 1066 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: 0.29 (0.43), residues: 420 helix: 0.78 (0.30), residues: 327 sheet: None (None), residues: 0 loop : -1.77 (0.61), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 246 HIS 0.007 0.001 HIS A 414 PHE 0.016 0.001 PHE A 299 TYR 0.010 0.001 TYR A 335 ARG 0.003 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.328 Fit side-chains REVERT: A 230 PHE cc_start: 0.4985 (m-80) cc_final: 0.4557 (m-10) REVERT: A 244 TRP cc_start: 0.3185 (t60) cc_final: 0.2467 (t60) REVERT: A 247 LEU cc_start: 0.6669 (mt) cc_final: 0.6219 (pp) REVERT: A 342 MET cc_start: 0.5783 (ttm) cc_final: 0.5446 (mtm) REVERT: A 432 PHE cc_start: 0.3628 (m-80) cc_final: 0.2892 (m-10) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1517 time to fit residues: 10.4449 Evaluate side-chains 34 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.7980 chunk 31 optimal weight: 0.0980 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN A 207 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.209939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.175979 restraints weight = 4599.746| |-----------------------------------------------------------------------------| r_work (start): 0.4176 rms_B_bonded: 3.96 r_work (final): 0.4176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4387 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 3292 Z= 0.293 Angle : 0.764 6.871 4507 Z= 0.398 Chirality : 0.047 0.170 521 Planarity : 0.007 0.069 547 Dihedral : 5.253 18.884 448 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.18 % Allowed : 12.42 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.40), residues: 420 helix: -0.10 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -2.12 (0.60), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 103 HIS 0.007 0.003 HIS A 183 PHE 0.034 0.003 PHE A 116 TYR 0.013 0.002 TYR A 421 ARG 0.010 0.001 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.303 Fit side-chains REVERT: A 227 THR cc_start: 0.5788 (p) cc_final: 0.5123 (p) REVERT: A 244 TRP cc_start: 0.3754 (t60) cc_final: 0.2925 (t60) REVERT: A 316 MET cc_start: 0.6507 (mpp) cc_final: 0.5904 (mmm) REVERT: A 438 MET cc_start: 0.6693 (tmm) cc_final: 0.5914 (ttm) outliers start: 10 outliers final: 4 residues processed: 56 average time/residue: 0.1284 time to fit residues: 9.1288 Evaluate side-chains 42 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 117 TYR Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 380 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 16 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4789 r_free = 0.4789 target = 0.226705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.195557 restraints weight = 4301.885| |-----------------------------------------------------------------------------| r_work (start): 0.4365 rms_B_bonded: 3.16 r_work: 0.4197 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.4197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5596 moved from start: 0.7648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 3292 Z= 0.301 Angle : 0.732 6.858 4507 Z= 0.383 Chirality : 0.045 0.155 521 Planarity : 0.007 0.067 547 Dihedral : 5.103 25.023 448 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.52 % Favored : 95.24 % Rotamer: Outliers : 3.18 % Allowed : 19.43 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.39), residues: 420 helix: -0.13 (0.28), residues: 326 sheet: None (None), residues: 0 loop : -2.63 (0.54), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 103 HIS 0.006 0.002 HIS A 183 PHE 0.021 0.002 PHE A 299 TYR 0.031 0.002 TYR A 203 ARG 0.007 0.002 ARG A 365 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.305 Fit side-chains REVERT: A 117 TYR cc_start: 0.7456 (OUTLIER) cc_final: 0.6581 (t80) REVERT: A 203 TYR cc_start: 0.7640 (m-80) cc_final: 0.6916 (t80) REVERT: A 438 MET cc_start: 0.7602 (tmm) cc_final: 0.6966 (mtp) outliers start: 10 outliers final: 5 residues processed: 57 average time/residue: 0.1547 time to fit residues: 11.1763 Evaluate side-chains 47 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 117 TYR Chi-restraints excluded: chain A residue 228 TYR Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 473 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 23 optimal weight: 0.9980 chunk 7 optimal weight: 0.0980 chunk 35 optimal weight: 0.0570 chunk 37 optimal weight: 0.4980 chunk 12 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 38 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS A 225 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4764 r_free = 0.4764 target = 0.224238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.192562 restraints weight = 4306.206| |-----------------------------------------------------------------------------| r_work (start): 0.4374 rms_B_bonded: 3.15 r_work: 0.4233 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.4233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5630 moved from start: 0.8518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3292 Z= 0.197 Angle : 0.608 5.275 4507 Z= 0.312 Chirality : 0.041 0.131 521 Planarity : 0.006 0.052 547 Dihedral : 4.813 21.673 448 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.50 % Allowed : 21.34 % Favored : 75.16 % 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: -0.47 (0.41), residues: 420 helix: 0.31 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -2.27 (0.57), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 226 HIS 0.010 0.002 HIS A 183 PHE 0.019 0.002 PHE A 322 TYR 0.008 0.001 TYR A 421 ARG 0.012 0.001 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 165 ILE cc_start: 0.8384 (tp) cc_final: 0.8170 (tp) REVERT: A 203 TYR cc_start: 0.7540 (OUTLIER) cc_final: 0.7091 (t80) REVERT: A 247 LEU cc_start: 0.7190 (OUTLIER) cc_final: 0.6979 (mm) REVERT: A 432 PHE cc_start: 0.7462 (OUTLIER) cc_final: 0.6652 (t80) REVERT: A 438 MET cc_start: 0.7630 (tmm) cc_final: 0.7244 (mtp) REVERT: A 473 PHE cc_start: 0.6708 (OUTLIER) cc_final: 0.6458 (m-80) outliers start: 11 outliers final: 4 residues processed: 49 average time/residue: 0.1205 time to fit residues: 7.6763 Evaluate side-chains 45 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 117 TYR Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 473 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 32 optimal weight: 2.9990 chunk 41 optimal weight: 0.2980 chunk 13 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 21 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS A 430 ASN A 488 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.192038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.157722 restraints weight = 5006.181| |-----------------------------------------------------------------------------| r_work (start): 0.4205 rms_B_bonded: 3.49 r_work: 0.4043 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 1.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 3292 Z= 0.357 Angle : 0.824 9.536 4507 Z= 0.436 Chirality : 0.050 0.171 521 Planarity : 0.007 0.062 547 Dihedral : 5.520 20.983 448 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 6.05 % Allowed : 23.57 % Favored : 70.38 % 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: -1.56 (0.37), residues: 420 helix: -0.50 (0.27), residues: 312 sheet: None (None), residues: 0 loop : -2.30 (0.51), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 240 HIS 0.006 0.002 HIS A 414 PHE 0.027 0.003 PHE A 116 TYR 0.010 0.002 TYR A 40 ARG 0.006 0.001 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 56 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: A 203 TYR cc_start: 0.8069 (OUTLIER) cc_final: 0.7165 (t80) REVERT: A 228 TYR cc_start: 0.6264 (OUTLIER) cc_final: 0.5910 (t80) REVERT: A 361 LEU cc_start: 0.6252 (OUTLIER) cc_final: 0.5358 (tp) outliers start: 19 outliers final: 10 residues processed: 71 average time/residue: 0.1202 time to fit residues: 10.9244 Evaluate side-chains 58 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 TRP Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 189 TRP Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 228 TYR Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 458 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 7 optimal weight: 2.9990 chunk 35 optimal weight: 0.0470 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 21 optimal weight: 0.0170 chunk 15 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.5116 ------------------------------------------------------------------------------- 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 = 0.4536 r_free = 0.4536 target = 0.192670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.158673 restraints weight = 5078.268| |-----------------------------------------------------------------------------| r_work (start): 0.4245 rms_B_bonded: 3.55 r_work: 0.4083 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 moved from start: 1.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 3292 Z= 0.234 Angle : 0.661 10.733 4507 Z= 0.336 Chirality : 0.045 0.281 521 Planarity : 0.006 0.059 547 Dihedral : 5.188 20.129 448 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 5.10 % Allowed : 24.52 % Favored : 70.38 % 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: -0.96 (0.40), residues: 420 helix: -0.07 (0.29), residues: 320 sheet: None (None), residues: 0 loop : -2.23 (0.54), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 189 HIS 0.008 0.002 HIS A 414 PHE 0.021 0.002 PHE A 322 TYR 0.021 0.001 TYR A 203 ARG 0.013 0.001 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: A 39 ARG cc_start: 0.7699 (ttm110) cc_final: 0.7266 (ttm110) REVERT: A 185 MET cc_start: 0.7350 (tpt) cc_final: 0.7149 (tpt) REVERT: A 189 TRP cc_start: 0.7602 (OUTLIER) cc_final: 0.5062 (t60) REVERT: A 203 TYR cc_start: 0.7518 (OUTLIER) cc_final: 0.6852 (t80) REVERT: A 228 TYR cc_start: 0.6436 (OUTLIER) cc_final: 0.6141 (t80) REVERT: A 250 ASP cc_start: 0.6510 (t0) cc_final: 0.6065 (t0) outliers start: 16 outliers final: 10 residues processed: 67 average time/residue: 0.1014 time to fit residues: 9.0088 Evaluate side-chains 60 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 103 TRP Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 189 TRP Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 228 TYR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 473 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 12 optimal weight: 0.0470 chunk 28 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.191650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.157748 restraints weight = 4956.352| |-----------------------------------------------------------------------------| r_work (start): 0.4224 rms_B_bonded: 3.51 r_work: 0.4059 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6796 moved from start: 1.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3292 Z= 0.217 Angle : 0.687 9.517 4507 Z= 0.338 Chirality : 0.045 0.173 521 Planarity : 0.006 0.060 547 Dihedral : 5.072 19.808 448 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 5.41 % Allowed : 26.43 % Favored : 68.15 % 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: -0.86 (0.40), residues: 420 helix: 0.01 (0.29), residues: 316 sheet: None (None), residues: 0 loop : -2.10 (0.54), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 244 HIS 0.008 0.001 HIS A 414 PHE 0.024 0.002 PHE A 322 TYR 0.007 0.001 TYR A 306 ARG 0.006 0.001 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 39 ARG cc_start: 0.7799 (ttm110) cc_final: 0.7333 (ttm110) REVERT: A 128 TYR cc_start: 0.8172 (t80) cc_final: 0.7003 (m-10) REVERT: A 137 MET cc_start: 0.6987 (mpp) cc_final: 0.6583 (mmt) REVERT: A 182 MET cc_start: 0.6507 (tmm) cc_final: 0.6235 (tmm) REVERT: A 189 TRP cc_start: 0.7891 (OUTLIER) cc_final: 0.5085 (t60) REVERT: A 203 TYR cc_start: 0.6736 (OUTLIER) cc_final: 0.6061 (t80) REVERT: A 250 ASP cc_start: 0.6503 (t0) cc_final: 0.6107 (t0) outliers start: 17 outliers final: 9 residues processed: 68 average time/residue: 0.1155 time to fit residues: 10.3587 Evaluate side-chains 59 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 103 TRP Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 189 TRP Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 442 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4492 r_free = 0.4492 target = 0.193669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.158939 restraints weight = 4665.214| |-----------------------------------------------------------------------------| r_work (start): 0.4338 rms_B_bonded: 3.17 r_work: 0.4223 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.4223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6781 moved from start: 1.4606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3292 Z= 0.261 Angle : 0.690 10.380 4507 Z= 0.347 Chirality : 0.045 0.166 521 Planarity : 0.006 0.060 547 Dihedral : 5.101 20.046 448 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 4.46 % Allowed : 29.94 % Favored : 65.61 % 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: -0.83 (0.40), residues: 420 helix: 0.06 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -2.29 (0.52), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 226 HIS 0.008 0.002 HIS A 414 PHE 0.025 0.002 PHE A 241 TYR 0.010 0.001 TYR A 203 ARG 0.008 0.001 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.336 Fit side-chains REVERT: A 39 ARG cc_start: 0.7871 (ttm110) cc_final: 0.7391 (ttp-110) REVERT: A 128 TYR cc_start: 0.8091 (t80) cc_final: 0.6685 (m-10) REVERT: A 137 MET cc_start: 0.6822 (mpp) cc_final: 0.6568 (mmt) REVERT: A 189 TRP cc_start: 0.7931 (OUTLIER) cc_final: 0.4909 (t60) REVERT: A 203 TYR cc_start: 0.6723 (OUTLIER) cc_final: 0.6000 (t80) REVERT: A 250 ASP cc_start: 0.6680 (t0) cc_final: 0.6335 (t0) REVERT: A 438 MET cc_start: 0.6923 (mtp) cc_final: 0.6704 (mtm) outliers start: 14 outliers final: 8 residues processed: 66 average time/residue: 0.1253 time to fit residues: 10.7347 Evaluate side-chains 62 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 189 TRP Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 442 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 23 optimal weight: 1.9990 chunk 2 optimal weight: 0.2980 chunk 15 optimal weight: 0.5980 chunk 41 optimal weight: 0.0170 chunk 38 optimal weight: 0.4980 chunk 33 optimal weight: 0.5980 chunk 37 optimal weight: 0.0270 chunk 1 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.2876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.212248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.176699 restraints weight = 4574.112| |-----------------------------------------------------------------------------| r_work (start): 0.4470 rms_B_bonded: 3.51 r_work: 0.4341 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.4341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 moved from start: 1.4865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 3292 Z= 0.189 Angle : 0.641 10.236 4507 Z= 0.318 Chirality : 0.042 0.155 521 Planarity : 0.006 0.062 547 Dihedral : 4.942 19.324 448 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.18 % Allowed : 31.85 % Favored : 64.97 % 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: -0.49 (0.41), residues: 420 helix: 0.32 (0.30), residues: 309 sheet: None (None), residues: 0 loop : -2.01 (0.52), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 244 HIS 0.009 0.001 HIS A 414 PHE 0.023 0.001 PHE A 322 TYR 0.008 0.001 TYR A 306 ARG 0.006 0.001 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.257 Fit side-chains REVERT: A 39 ARG cc_start: 0.7891 (ttm110) cc_final: 0.7305 (ttm110) REVERT: A 128 TYR cc_start: 0.7879 (t80) cc_final: 0.6662 (m-10) REVERT: A 189 TRP cc_start: 0.7881 (OUTLIER) cc_final: 0.4821 (t60) REVERT: A 203 TYR cc_start: 0.6700 (OUTLIER) cc_final: 0.5918 (t80) REVERT: A 250 ASP cc_start: 0.6706 (t0) cc_final: 0.6387 (t0) REVERT: A 284 PRO cc_start: 0.6956 (Cg_exo) cc_final: 0.6686 (Cg_endo) REVERT: A 316 MET cc_start: 0.7304 (mmm) cc_final: 0.7097 (mtt) REVERT: A 438 MET cc_start: 0.6971 (mtp) cc_final: 0.6685 (mtm) outliers start: 10 outliers final: 6 residues processed: 66 average time/residue: 0.1360 time to fit residues: 11.1728 Evaluate side-chains 62 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 189 TRP Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 442 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 26 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 27 optimal weight: 0.3980 chunk 7 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 21 optimal weight: 0.0000 chunk 31 optimal weight: 0.9990 chunk 19 optimal weight: 0.0040 overall best weight: 0.3996 ------------------------------------------------------------------------------- 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 = 0.4507 r_free = 0.4507 target = 0.195565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.162642 restraints weight = 4464.689| |-----------------------------------------------------------------------------| r_work (start): 0.4375 rms_B_bonded: 3.11 r_work: 0.4245 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.4245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 1.5080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3292 Z= 0.207 Angle : 0.711 11.569 4507 Z= 0.337 Chirality : 0.042 0.132 521 Planarity : 0.006 0.061 547 Dihedral : 4.923 19.342 448 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.23 % Allowed : 33.12 % Favored : 64.65 % 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: -0.38 (0.41), residues: 420 helix: 0.39 (0.30), residues: 311 sheet: None (None), residues: 0 loop : -1.96 (0.53), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 240 HIS 0.007 0.002 HIS A 414 PHE 0.022 0.001 PHE A 322 TYR 0.014 0.001 TYR A 54 ARG 0.006 0.001 ARG A 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.327 Fit side-chains REVERT: A 39 ARG cc_start: 0.7974 (ttm110) cc_final: 0.7626 (ttp-110) REVERT: A 128 TYR cc_start: 0.7835 (t80) cc_final: 0.6635 (m-10) REVERT: A 189 TRP cc_start: 0.7887 (OUTLIER) cc_final: 0.4960 (t60) REVERT: A 203 TYR cc_start: 0.6567 (OUTLIER) cc_final: 0.5901 (t80) REVERT: A 250 ASP cc_start: 0.6698 (t0) cc_final: 0.6384 (t0) REVERT: A 284 PRO cc_start: 0.7101 (Cg_exo) cc_final: 0.6843 (Cg_endo) REVERT: A 438 MET cc_start: 0.7053 (mtp) cc_final: 0.6816 (mtm) outliers start: 7 outliers final: 5 residues processed: 61 average time/residue: 0.1126 time to fit residues: 9.0399 Evaluate side-chains 59 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 189 TRP Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 442 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 0.0870 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 41 optimal weight: 0.0030 chunk 21 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 overall best weight: 0.4968 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.195624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.161082 restraints weight = 4579.701| |-----------------------------------------------------------------------------| r_work (start): 0.4132 rms_B_bonded: 3.12 r_work: 0.3990 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 1.5608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3292 Z= 0.215 Angle : 0.702 10.356 4507 Z= 0.342 Chirality : 0.043 0.168 521 Planarity : 0.006 0.062 547 Dihedral : 4.897 20.859 448 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.87 % Allowed : 32.17 % Favored : 64.97 % 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: -0.24 (0.41), residues: 420 helix: 0.46 (0.30), residues: 312 sheet: None (None), residues: 0 loop : -1.79 (0.54), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 186 HIS 0.012 0.002 HIS A 414 PHE 0.023 0.001 PHE A 322 TYR 0.008 0.001 TYR A 54 ARG 0.005 0.001 ARG A 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1752.37 seconds wall clock time: 30 minutes 51.00 seconds (1851.00 seconds total)