Starting phenix.real_space_refine on Wed Mar 5 18:46:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6jnd_9848/03_2025/6jnd_9848.cif Found real_map, /net/cci-nas-00/data/ceres_data/6jnd_9848/03_2025/6jnd_9848.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6jnd_9848/03_2025/6jnd_9848.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6jnd_9848/03_2025/6jnd_9848.map" model { file = "/net/cci-nas-00/data/ceres_data/6jnd_9848/03_2025/6jnd_9848.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6jnd_9848/03_2025/6jnd_9848.cif" } resolution = 3.9 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= 0.013 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 15 5.16 5 C 2103 2.51 5 N 561 2.21 5 O 615 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 3294 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3286 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 398} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'TRS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.62, per 1000 atoms: 0.80 Number of scatterers: 3294 At special positions: 0 Unit cell: (71.34, 73.08, 73.95, 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 15 16.00 O 615 8.00 N 561 7.00 C 2103 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: 0.75 Conformation dependent library (CDL) restraints added in 368.1 milliseconds 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 764 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 3 sheets defined 48.4% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 5 through 17 removed outlier: 3.755A pdb=" N ALA A 10 " --> pdb=" O PRO A 6 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU A 14 " --> pdb=" O ALA A 10 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG A 16 " --> pdb=" O LYS A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 95 removed outlier: 3.826A pdb=" N ALA A 85 " --> pdb=" O SER A 81 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 86 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N TRP A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS A 93 " --> pdb=" O TRP A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 115 removed outlier: 3.943A pdb=" N LEU A 115 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 129 removed outlier: 3.586A pdb=" N ARG A 122 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA A 126 " --> pdb=" O ARG A 122 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE A 128 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG A 129 " --> pdb=" O ARG A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 135 removed outlier: 3.629A pdb=" N ILE A 135 " --> pdb=" O TYR A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 165 removed outlier: 3.536A pdb=" N GLY A 154 " --> pdb=" O PRO A 150 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TRP A 155 " --> pdb=" O LYS A 151 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET A 157 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE A 163 " --> pdb=" O GLU A 159 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG A 165 " --> pdb=" O GLU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 173 removed outlier: 3.540A pdb=" N VAL A 173 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 207 removed outlier: 3.572A pdb=" N THR A 198 " --> pdb=" O GLY A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 234 removed outlier: 3.552A pdb=" N TYR A 226 " --> pdb=" O ASN A 222 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 228 " --> pdb=" O GLY A 224 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 265 Processing helix chain 'A' and resid 280 through 286 removed outlier: 3.549A pdb=" N LEU A 284 " --> pdb=" O THR A 280 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 286' Processing helix chain 'A' and resid 326 through 332 Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 345 through 361 removed outlier: 3.943A pdb=" N SER A 351 " --> pdb=" O GLY A 347 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TRP A 355 " --> pdb=" O SER A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 392 removed outlier: 4.005A pdb=" N ASP A 374 " --> pdb=" O ARG A 370 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS A 375 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS A 379 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL A 384 " --> pdb=" O ALA A 380 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR A 387 " --> pdb=" O GLU A 383 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP A 390 " --> pdb=" O ASN A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 412 removed outlier: 4.125A pdb=" N TYR A 400 " --> pdb=" O ARG A 396 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL A 401 " --> pdb=" O ASP A 397 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA A 410 " --> pdb=" O ARG A 406 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 45 removed outlier: 3.604A pdb=" N GLY A 107 " --> pdb=" O PHE A 57 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 68 through 69 removed outlier: 6.798A pdb=" N THR A 68 " --> pdb=" O ILE A 141 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 248 through 250 removed outlier: 7.420A pdb=" N VAL A 217 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL A 242 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N LYS A 214 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N ALA A 293 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ALA A 216 " --> pdb=" O ALA A 293 " (cutoff:3.500A) 120 hydrogen bonds defined for protein. 348 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: 0.80 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1073 1.34 - 1.46: 611 1.46 - 1.57: 1653 1.57 - 1.69: 0 1.69 - 1.81: 29 Bond restraints: 3366 Sorted by residual: bond pdb=" N TRS A 901 " pdb=" C TRS A 901 " ideal model delta sigma weight residual 1.501 1.462 0.039 2.00e-02 2.50e+03 3.87e+00 bond pdb=" C LYS A 177 " pdb=" N PRO A 178 " ideal model delta sigma weight residual 1.330 1.346 -0.016 1.25e-02 6.40e+03 1.59e+00 bond pdb=" CB ASN A 62 " pdb=" CG ASN A 62 " ideal model delta sigma weight residual 1.516 1.485 0.031 2.50e-02 1.60e+03 1.54e+00 bond pdb=" CA ARG A 36 " pdb=" C ARG A 36 " ideal model delta sigma weight residual 1.529 1.516 0.013 1.04e-02 9.25e+03 1.52e+00 bond pdb=" CA ASP A 145 " pdb=" CB ASP A 145 " ideal model delta sigma weight residual 1.539 1.525 0.014 1.36e-02 5.41e+03 1.11e+00 ... (remaining 3361 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 4153 1.38 - 2.76: 363 2.76 - 4.14: 34 4.14 - 5.53: 11 5.53 - 6.91: 1 Bond angle restraints: 4562 Sorted by residual: angle pdb=" N ILE A 181 " pdb=" CA ILE A 181 " pdb=" C ILE A 181 " ideal model delta sigma weight residual 113.20 106.29 6.91 9.60e-01 1.09e+00 5.18e+01 angle pdb=" N VAL A 97 " pdb=" CA VAL A 97 " pdb=" C VAL A 97 " ideal model delta sigma weight residual 112.83 108.49 4.34 9.90e-01 1.02e+00 1.93e+01 angle pdb=" CA ALA A 143 " pdb=" C ALA A 143 " pdb=" N PRO A 144 " ideal model delta sigma weight residual 117.96 120.68 -2.72 8.10e-01 1.52e+00 1.13e+01 angle pdb=" C VAL A 146 " pdb=" N TYR A 147 " pdb=" CA TYR A 147 " ideal model delta sigma weight residual 123.05 127.68 -4.63 1.57e+00 4.06e-01 8.70e+00 angle pdb=" C LYS A 271 " pdb=" N ASP A 272 " pdb=" CA ASP A 272 " ideal model delta sigma weight residual 122.40 126.57 -4.17 1.45e+00 4.76e-01 8.27e+00 ... (remaining 4557 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 1785 17.36 - 34.72: 165 34.72 - 52.07: 51 52.07 - 69.43: 10 69.43 - 86.79: 5 Dihedral angle restraints: 2016 sinusoidal: 818 harmonic: 1198 Sorted by residual: dihedral pdb=" CA TYR A 147 " pdb=" C TYR A 147 " pdb=" N THR A 148 " pdb=" CA THR A 148 " ideal model delta harmonic sigma weight residual 180.00 163.96 16.04 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" CB GLU A 367 " pdb=" CG GLU A 367 " pdb=" CD GLU A 367 " pdb=" OE1 GLU A 367 " ideal model delta sinusoidal sigma weight residual 0.00 -86.79 86.79 1 3.00e+01 1.11e-03 1.01e+01 dihedral pdb=" CB GLU A 78 " pdb=" CG GLU A 78 " pdb=" CD GLU A 78 " pdb=" OE1 GLU A 78 " ideal model delta sinusoidal sigma weight residual 0.00 -86.79 86.79 1 3.00e+01 1.11e-03 1.01e+01 ... (remaining 2013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 266 0.034 - 0.068: 160 0.068 - 0.102: 41 0.102 - 0.136: 27 0.136 - 0.170: 3 Chirality restraints: 497 Sorted by residual: chirality pdb=" CB ILE A 174 " pdb=" CA ILE A 174 " pdb=" CG1 ILE A 174 " pdb=" CG2 ILE A 174 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.27e-01 chirality pdb=" CA ILE A 108 " pdb=" N ILE A 108 " pdb=" C ILE A 108 " pdb=" CB ILE A 108 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.13e-01 chirality pdb=" CA TYR A 147 " pdb=" N TYR A 147 " pdb=" C TYR A 147 " pdb=" CB TYR A 147 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.17e-01 ... (remaining 494 not shown) Planarity restraints: 584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 141 " 0.038 5.00e-02 4.00e+02 5.84e-02 5.46e+00 pdb=" N PRO A 142 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 142 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 142 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 5 " 0.037 5.00e-02 4.00e+02 5.54e-02 4.92e+00 pdb=" N PRO A 6 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 6 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 6 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 149 " 0.035 5.00e-02 4.00e+02 5.24e-02 4.40e+00 pdb=" N PRO A 150 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 150 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 150 " 0.029 5.00e-02 4.00e+02 ... (remaining 581 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 1093 2.83 - 3.35: 2726 3.35 - 3.87: 5053 3.87 - 4.38: 5857 4.38 - 4.90: 10120 Nonbonded interactions: 24849 Sorted by model distance: nonbonded pdb=" O ALA A 223 " pdb=" OG1 THR A 227 " model vdw 2.316 3.040 nonbonded pdb=" OG1 THR A 365 " pdb=" OE1 GLU A 368 " model vdw 2.324 3.040 nonbonded pdb=" O2 TRS A 901 " pdb=" O3 TRS A 901 " model vdw 2.337 3.040 nonbonded pdb=" N ASP A 256 " pdb=" OD1 ASP A 256 " model vdw 2.346 3.120 nonbonded pdb=" O ASP A 340 " pdb=" ND2 ASN A 344 " model vdw 2.357 3.120 ... (remaining 24844 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: 0.010 Normalize map: mean=0, sd=1: 0.710 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.570 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 3366 Z= 0.384 Angle : 0.825 6.907 4562 Z= 0.538 Chirality : 0.050 0.170 497 Planarity : 0.007 0.058 584 Dihedral : 15.637 86.791 1252 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 11.73 % Allowed : 11.14 % Favored : 77.13 % 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: -5.73 (0.30), residues: 417 helix: -4.79 (0.14), residues: 183 sheet: -2.24 (0.72), residues: 46 loop : -3.00 (0.38), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 30 HIS 0.003 0.001 HIS A 61 PHE 0.011 0.001 PHE A 341 TYR 0.006 0.002 TYR A 160 ARG 0.003 0.001 ARG A 58 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 78 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7330 (pt0) cc_final: 0.6688 (tt0) REVERT: A 90 MET cc_start: 0.8581 (tpt) cc_final: 0.7870 (tpt) REVERT: A 118 ARG cc_start: 0.7903 (mtp85) cc_final: 0.7288 (mpp80) REVERT: A 189 THR cc_start: 0.7667 (p) cc_final: 0.7465 (t) REVERT: A 193 GLN cc_start: 0.7386 (tp40) cc_final: 0.6650 (tt0) REVERT: A 307 ASP cc_start: 0.5233 (OUTLIER) cc_final: 0.4767 (t70) REVERT: A 388 HIS cc_start: 0.7906 (t70) cc_final: 0.7548 (t70) outliers start: 40 outliers final: 8 residues processed: 110 average time/residue: 0.1608 time to fit residues: 21.5744 Evaluate side-chains 64 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 308 ASN Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 397 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.2980 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN A 267 HIS A 358 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.123956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.093843 restraints weight = 5837.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.094691 restraints weight = 4493.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.095415 restraints weight = 3806.798| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3366 Z= 0.142 Angle : 0.520 5.546 4562 Z= 0.282 Chirality : 0.045 0.173 497 Planarity : 0.005 0.043 584 Dihedral : 6.220 48.823 473 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.52 % Allowed : 18.77 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.95 (0.34), residues: 417 helix: -3.01 (0.26), residues: 190 sheet: -1.44 (0.71), residues: 52 loop : -2.34 (0.43), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 63 HIS 0.003 0.001 HIS A 267 PHE 0.023 0.002 PHE A 273 TYR 0.019 0.001 TYR A 132 ARG 0.005 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: A 9 MET cc_start: 0.8022 (tpp) cc_final: 0.7804 (mmm) REVERT: A 26 GLU cc_start: 0.7421 (pt0) cc_final: 0.6817 (tt0) REVERT: A 90 MET cc_start: 0.8384 (tpt) cc_final: 0.8065 (tpp) REVERT: A 132 TYR cc_start: 0.8561 (t80) cc_final: 0.6179 (p90) REVERT: A 189 THR cc_start: 0.7880 (p) cc_final: 0.7579 (t) REVERT: A 193 GLN cc_start: 0.7451 (tp40) cc_final: 0.6686 (tt0) REVERT: A 287 LEU cc_start: 0.5804 (OUTLIER) cc_final: 0.5587 (tt) outliers start: 12 outliers final: 3 residues processed: 71 average time/residue: 0.1779 time to fit residues: 15.4946 Evaluate side-chains 54 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 348 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 35 optimal weight: 4.9990 chunk 2 optimal weight: 0.0980 chunk 13 optimal weight: 0.0270 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 33 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 30 optimal weight: 30.0000 chunk 34 optimal weight: 6.9990 overall best weight: 0.9642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 ASN ** A 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.124501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.094387 restraints weight = 5730.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.094994 restraints weight = 4479.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.095074 restraints weight = 3747.107| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 3366 Z= 0.147 Angle : 0.496 6.289 4562 Z= 0.261 Chirality : 0.043 0.139 497 Planarity : 0.005 0.051 584 Dihedral : 4.572 37.678 459 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.35 % Allowed : 19.94 % Favored : 77.71 % 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: -2.50 (0.38), residues: 417 helix: -1.44 (0.35), residues: 179 sheet: -1.43 (0.66), residues: 62 loop : -1.81 (0.43), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.002 0.000 HIS A 388 PHE 0.009 0.001 PHE A 341 TYR 0.012 0.001 TYR A 132 ARG 0.004 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.384 Fit side-chains REVERT: A 26 GLU cc_start: 0.7719 (pt0) cc_final: 0.7083 (tt0) REVERT: A 90 MET cc_start: 0.8518 (tpt) cc_final: 0.7863 (tpt) REVERT: A 189 THR cc_start: 0.7967 (p) cc_final: 0.7549 (t) REVERT: A 193 GLN cc_start: 0.7330 (tp40) cc_final: 0.6527 (tt0) REVERT: A 226 TYR cc_start: 0.7409 (m-80) cc_final: 0.7155 (m-80) outliers start: 8 outliers final: 3 residues processed: 60 average time/residue: 0.1339 time to fit residues: 10.2993 Evaluate side-chains 47 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 413 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 9.9990 chunk 24 optimal weight: 40.0000 chunk 13 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 18 optimal weight: 20.0000 chunk 4 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 ASN ** A 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.121712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.091318 restraints weight = 5932.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.091834 restraints weight = 4754.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.091940 restraints weight = 4120.884| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.6088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3366 Z= 0.184 Angle : 0.543 9.519 4562 Z= 0.279 Chirality : 0.045 0.134 497 Planarity : 0.004 0.035 584 Dihedral : 4.604 29.134 458 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.64 % Allowed : 20.23 % Favored : 77.13 % 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: -2.03 (0.39), residues: 417 helix: -0.76 (0.37), residues: 183 sheet: -1.36 (0.70), residues: 56 loop : -1.87 (0.44), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 63 HIS 0.003 0.001 HIS A 388 PHE 0.015 0.002 PHE A 341 TYR 0.009 0.001 TYR A 132 ARG 0.003 0.001 ARG A 125 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.394 Fit side-chains REVERT: A 90 MET cc_start: 0.8873 (tpt) cc_final: 0.8147 (tpt) REVERT: A 189 THR cc_start: 0.8129 (p) cc_final: 0.7648 (t) REVERT: A 193 GLN cc_start: 0.7644 (tp40) cc_final: 0.6679 (tt0) REVERT: A 237 MET cc_start: 0.6790 (mmm) cc_final: 0.6070 (mmt) REVERT: A 304 LYS cc_start: 0.6770 (mttm) cc_final: 0.6166 (mmtt) outliers start: 9 outliers final: 6 residues processed: 52 average time/residue: 0.1607 time to fit residues: 10.4346 Evaluate side-chains 41 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 413 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 6 optimal weight: 9.9990 chunk 30 optimal weight: 30.0000 chunk 13 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 31 optimal weight: 7.9990 chunk 14 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 30.0000 chunk 40 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3501 r_free = 0.3501 target = 0.123069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.092424 restraints weight = 5804.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.093091 restraints weight = 4529.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.093607 restraints weight = 3910.674| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.6466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3366 Z= 0.139 Angle : 0.464 5.969 4562 Z= 0.241 Chirality : 0.044 0.130 497 Planarity : 0.004 0.035 584 Dihedral : 4.248 30.771 458 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.35 % Allowed : 21.41 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.40), residues: 417 helix: -0.08 (0.38), residues: 178 sheet: -1.02 (0.69), residues: 62 loop : -1.47 (0.44), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 63 HIS 0.003 0.001 HIS A 388 PHE 0.010 0.001 PHE A 341 TYR 0.007 0.001 TYR A 132 ARG 0.002 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.384 Fit side-chains REVERT: A 90 MET cc_start: 0.8799 (tpt) cc_final: 0.8122 (tpt) REVERT: A 157 MET cc_start: 0.8712 (tmm) cc_final: 0.8412 (tmm) REVERT: A 189 THR cc_start: 0.8150 (p) cc_final: 0.7587 (t) outliers start: 8 outliers final: 3 residues processed: 52 average time/residue: 0.1503 time to fit residues: 9.8572 Evaluate side-chains 42 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 413 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 21 optimal weight: 8.9990 chunk 20 optimal weight: 20.0000 chunk 18 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.115792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.085412 restraints weight = 6156.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.086075 restraints weight = 4979.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.086295 restraints weight = 4324.300| |-----------------------------------------------------------------------------| r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.7378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 3366 Z= 0.417 Angle : 0.634 5.912 4562 Z= 0.339 Chirality : 0.050 0.139 497 Planarity : 0.004 0.035 584 Dihedral : 5.546 35.452 458 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.52 % Allowed : 22.87 % Favored : 73.61 % 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: -1.81 (0.40), residues: 417 helix: -0.61 (0.38), residues: 179 sheet: -1.32 (0.72), residues: 52 loop : -1.67 (0.45), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 30 HIS 0.002 0.001 HIS A 394 PHE 0.017 0.002 PHE A 381 TYR 0.013 0.002 TYR A 385 ARG 0.004 0.001 ARG A 58 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.368 Fit side-chains REVERT: A 90 MET cc_start: 0.8832 (tpt) cc_final: 0.8346 (tpt) REVERT: A 118 ARG cc_start: 0.7904 (mtp85) cc_final: 0.7455 (mpp80) REVERT: A 232 LYS cc_start: 0.7981 (tppt) cc_final: 0.7713 (tmmt) REVERT: A 348 VAL cc_start: 0.9017 (OUTLIER) cc_final: 0.8779 (t) REVERT: A 395 MET cc_start: 0.7895 (mmt) cc_final: 0.7603 (mmt) outliers start: 12 outliers final: 9 residues processed: 47 average time/residue: 0.1555 time to fit residues: 9.1510 Evaluate side-chains 46 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 382 TRP Chi-restraints excluded: chain A residue 397 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 33 optimal weight: 0.0970 chunk 16 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 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 = 0.3456 r_free = 0.3456 target = 0.118984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.088870 restraints weight = 5843.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.089482 restraints weight = 4739.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.089727 restraints weight = 4156.505| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.7543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3366 Z= 0.191 Angle : 0.499 5.649 4562 Z= 0.262 Chirality : 0.045 0.133 497 Planarity : 0.004 0.033 584 Dihedral : 4.956 34.195 458 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.76 % Allowed : 25.22 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.40), residues: 417 helix: -0.19 (0.38), residues: 182 sheet: -1.53 (0.70), residues: 52 loop : -1.63 (0.44), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 63 HIS 0.006 0.001 HIS A 394 PHE 0.013 0.001 PHE A 341 TYR 0.006 0.001 TYR A 101 ARG 0.002 0.000 ARG A 125 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.353 Fit side-chains REVERT: A 118 ARG cc_start: 0.7840 (mtp85) cc_final: 0.7462 (mpp80) outliers start: 6 outliers final: 5 residues processed: 47 average time/residue: 0.1880 time to fit residues: 10.6070 Evaluate side-chains 43 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 382 TRP Chi-restraints excluded: chain A residue 397 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 14 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 9 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 chunk 27 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 15 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.116642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.087106 restraints weight = 5932.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.087652 restraints weight = 4857.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.088073 restraints weight = 4258.707| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.7756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3366 Z= 0.260 Angle : 0.533 5.500 4562 Z= 0.282 Chirality : 0.046 0.144 497 Planarity : 0.004 0.033 584 Dihedral : 4.925 31.992 458 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.52 % Allowed : 24.34 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.41), residues: 417 helix: -0.04 (0.38), residues: 177 sheet: -1.62 (0.69), residues: 52 loop : -1.41 (0.46), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 63 HIS 0.008 0.002 HIS A 394 PHE 0.013 0.001 PHE A 341 TYR 0.008 0.001 TYR A 101 ARG 0.003 0.000 ARG A 125 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.363 Fit side-chains REVERT: A 46 MET cc_start: 0.8893 (mmm) cc_final: 0.8567 (mmm) REVERT: A 118 ARG cc_start: 0.7875 (mtp85) cc_final: 0.7469 (mpp80) outliers start: 12 outliers final: 9 residues processed: 52 average time/residue: 0.1569 time to fit residues: 10.2443 Evaluate side-chains 49 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 382 TRP Chi-restraints excluded: chain A residue 397 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 27 optimal weight: 0.1980 chunk 6 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 31 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 GLN ** A 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.118448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.088558 restraints weight = 5962.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.089145 restraints weight = 4786.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.089639 restraints weight = 4157.179| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.7851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3366 Z= 0.185 Angle : 0.522 7.164 4562 Z= 0.274 Chirality : 0.044 0.126 497 Planarity : 0.004 0.034 584 Dihedral : 4.654 33.806 458 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.93 % Allowed : 24.34 % Favored : 72.73 % 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: -1.13 (0.41), residues: 417 helix: 0.20 (0.39), residues: 177 sheet: -1.46 (0.68), residues: 58 loop : -1.39 (0.47), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 63 HIS 0.009 0.002 HIS A 394 PHE 0.011 0.001 PHE A 341 TYR 0.006 0.001 TYR A 101 ARG 0.002 0.000 ARG A 125 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.381 Fit side-chains REVERT: A 46 MET cc_start: 0.8900 (mmm) cc_final: 0.8565 (mmm) REVERT: A 118 ARG cc_start: 0.7789 (mtp85) cc_final: 0.7457 (mpp80) REVERT: A 157 MET cc_start: 0.8749 (tmm) cc_final: 0.8483 (tmm) REVERT: A 370 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7375 (tpp-160) outliers start: 10 outliers final: 5 residues processed: 48 average time/residue: 0.1924 time to fit residues: 11.3211 Evaluate side-chains 46 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 370 ARG Chi-restraints excluded: chain A residue 397 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 17 optimal weight: 0.3980 chunk 18 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 25 optimal weight: 8.9990 chunk 40 optimal weight: 7.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS ** A 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.116474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.086752 restraints weight = 5879.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.087414 restraints weight = 4778.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.087763 restraints weight = 4208.240| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.7968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3366 Z= 0.245 Angle : 0.546 6.408 4562 Z= 0.288 Chirality : 0.046 0.128 497 Planarity : 0.004 0.034 584 Dihedral : 4.784 32.415 458 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.93 % Allowed : 23.75 % Favored : 73.31 % 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: -1.23 (0.41), residues: 417 helix: 0.12 (0.39), residues: 177 sheet: -1.55 (0.67), residues: 58 loop : -1.43 (0.48), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 63 HIS 0.010 0.002 HIS A 394 PHE 0.013 0.001 PHE A 341 TYR 0.007 0.001 TYR A 101 ARG 0.002 0.000 ARG A 125 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.399 Fit side-chains REVERT: A 35 MET cc_start: 0.8280 (mtp) cc_final: 0.8073 (ttm) REVERT: A 46 MET cc_start: 0.8921 (mmm) cc_final: 0.8599 (mmm) REVERT: A 118 ARG cc_start: 0.7891 (mtp85) cc_final: 0.7471 (mpp80) REVERT: A 157 MET cc_start: 0.8819 (tmm) cc_final: 0.8553 (tmm) REVERT: A 210 LEU cc_start: 0.5069 (OUTLIER) cc_final: 0.4845 (mt) REVERT: A 370 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7393 (tpp-160) outliers start: 10 outliers final: 7 residues processed: 50 average time/residue: 0.1870 time to fit residues: 11.4188 Evaluate side-chains 48 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 370 ARG Chi-restraints excluded: chain A residue 397 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 13 optimal weight: 7.9990 chunk 4 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 28 optimal weight: 20.0000 chunk 20 optimal weight: 7.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 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 = 0.3433 r_free = 0.3433 target = 0.117744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.087931 restraints weight = 5975.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.088579 restraints weight = 4881.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.088890 restraints weight = 4177.392| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.8022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3366 Z= 0.201 Angle : 0.537 6.980 4562 Z= 0.282 Chirality : 0.045 0.127 497 Planarity : 0.004 0.035 584 Dihedral : 4.667 33.578 458 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.93 % Allowed : 23.17 % Favored : 73.90 % 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: -1.06 (0.41), residues: 417 helix: 0.27 (0.39), residues: 177 sheet: -1.43 (0.68), residues: 58 loop : -1.36 (0.47), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 63 HIS 0.010 0.002 HIS A 394 PHE 0.009 0.001 PHE A 341 TYR 0.006 0.001 TYR A 101 ARG 0.002 0.000 ARG A 125 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1344.58 seconds wall clock time: 24 minutes 15.13 seconds (1455.13 seconds total)