Starting phenix.real_space_refine on Tue Mar 3 11:30:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6jnd_9848/03_2026/6jnd_9848.cif Found real_map, /net/cci-nas-00/data/ceres_data/6jnd_9848/03_2026/6jnd_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 { model { file = "/net/cci-nas-00/data/ceres_data/6jnd_9848/03_2026/6jnd_9848.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6jnd_9848/03_2026/6jnd_9848.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6jnd_9848/03_2026/6jnd_9848.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6jnd_9848/03_2026/6jnd_9848.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 0.92, per 1000 atoms: 0.28 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: 0.25 Conformation dependent library (CDL) restraints added in 120.8 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: 0.10 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: 0.39 Time building geometry restraints manager: 0.32 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: 0.000 Normalize map: mean=0, sd=1: 0.980 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: 0.050 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.140 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.360 ------------------------------------------------------------------------------- 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= 0.268 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.003 0.001 ARG A 58 TYR 0.006 0.002 TYR A 160 PHE 0.011 0.001 PHE A 341 TRP 0.014 0.002 TRP A 30 HIS 0.003 0.001 HIS A 61 Details of bonding type rmsd covalent geometry : bond 0.00596 ( 3366) covalent geometry : angle 0.82481 ( 4562) hydrogen bonds : bond 0.32618 ( 120) hydrogen bonds : angle 9.69571 ( 348) *********************** 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 : 0.121 Fit side-chains revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7330 (pt0) cc_final: 0.6687 (tt0) REVERT: A 90 MET cc_start: 0.8581 (tpt) cc_final: 0.7884 (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: 0.7467 (t) REVERT: A 193 GLN cc_start: 0.7386 (tp40) cc_final: 0.6649 (tt0) REVERT: A 307 ASP cc_start: 0.5233 (OUTLIER) cc_final: 0.4765 (t70) REVERT: A 388 HIS cc_start: 0.7906 (t70) cc_final: 0.7547 (t70) outliers start: 40 outliers final: 8 residues processed: 110 average time/residue: 0.0604 time to fit residues: 8.0417 Evaluate side-chains 63 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.088 ------------------------------------------------------------------------------- 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 24 optimal weight: 9.9990 chunk 26 optimal weight: 0.0570 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 20.0000 chunk 25 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 overall best weight: 4.1304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 234 GLN A 267 HIS ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 GLN A 358 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.120457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.090031 restraints weight = 5920.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.090742 restraints weight = 4614.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.091309 restraints weight = 3946.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.091310 restraints weight = 3558.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.091840 restraints weight = 3553.902| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.4844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 3366 Z= 0.199 Angle : 0.613 5.044 4562 Z= 0.335 Chirality : 0.048 0.160 497 Planarity : 0.006 0.041 584 Dihedral : 7.073 56.539 473 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.69 % Allowed : 17.60 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.02 (0.35), residues: 417 helix: -3.01 (0.27), residues: 184 sheet: -1.69 (0.69), residues: 52 loop : -2.42 (0.43), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 246 TYR 0.020 0.002 TYR A 132 PHE 0.021 0.003 PHE A 273 TRP 0.013 0.002 TRP A 63 HIS 0.003 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 3366) covalent geometry : angle 0.61281 ( 4562) hydrogen bonds : bond 0.05000 ( 120) hydrogen bonds : angle 5.24864 ( 348) *********************** 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 65 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 0.121 Fit side-chains REVERT: A 90 MET cc_start: 0.8807 (tpt) cc_final: 0.8407 (tpt) REVERT: A 189 THR cc_start: 0.7993 (p) cc_final: 0.7483 (t) REVERT: A 337 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7935 (pt0) REVERT: A 348 VAL cc_start: 0.8469 (OUTLIER) cc_final: 0.8215 (t) REVERT: A 370 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.7511 (ttm110) REVERT: A 409 GLN cc_start: 0.9122 (tp40) cc_final: 0.8873 (mm-40) outliers start: 16 outliers final: 6 residues processed: 62 average time/residue: 0.0658 time to fit residues: 4.9180 Evaluate side-chains 45 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.115 ------------------------------------------------------------------------------- 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 173 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 370 ARG Chi-restraints excluded: chain A residue 397 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 9 optimal weight: 0.0270 chunk 20 optimal weight: 20.0000 chunk 15 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 11 optimal weight: 0.1980 chunk 34 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 28 optimal weight: 20.0000 chunk 30 optimal weight: 30.0000 overall best weight: 1.2444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 HIS 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 = 0.121498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.090734 restraints weight = 5935.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.091491 restraints weight = 4613.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.091731 restraints weight = 3986.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.092153 restraints weight = 3714.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.092549 restraints weight = 3491.816| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.5415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3366 Z= 0.093 Angle : 0.469 3.945 4562 Z= 0.252 Chirality : 0.044 0.141 497 Planarity : 0.004 0.038 584 Dihedral : 5.520 52.071 462 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.81 (0.38), residues: 417 helix: -1.62 (0.35), residues: 184 sheet: -1.25 (0.74), residues: 46 loop : -2.19 (0.43), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 246 TYR 0.012 0.001 TYR A 132 PHE 0.014 0.002 PHE A 273 TRP 0.009 0.001 TRP A 63 HIS 0.002 0.000 HIS A 394 Details of bonding type rmsd covalent geometry : bond 0.00209 ( 3366) covalent geometry : angle 0.46887 ( 4562) hydrogen bonds : bond 0.03602 ( 120) hydrogen bonds : angle 4.46967 ( 348) *********************** 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 51 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.115 Fit side-chains revert: symmetry clash REVERT: A 9 MET cc_start: 0.7906 (tpp) cc_final: 0.7675 (mmm) REVERT: A 90 MET cc_start: 0.8717 (tpt) cc_final: 0.8328 (tpt) REVERT: A 189 THR cc_start: 0.8040 (p) cc_final: 0.7594 (t) REVERT: A 370 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7415 (ttm110) REVERT: A 388 HIS cc_start: 0.8242 (OUTLIER) cc_final: 0.8016 (t70) REVERT: A 409 GLN cc_start: 0.9064 (tp40) cc_final: 0.8821 (mm-40) outliers start: 9 outliers final: 2 residues processed: 48 average time/residue: 0.0647 time to fit residues: 3.8718 Evaluate side-chains 41 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 370 ARG Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 6 optimal weight: 5.9990 chunk 29 optimal weight: 0.0170 chunk 40 optimal weight: 8.9990 chunk 9 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 overall best weight: 1.4026 ------------------------------------------------------------------------------- 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 = 0.3486 r_free = 0.3486 target = 0.121621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.092038 restraints weight = 5848.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.092238 restraints weight = 4656.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.092269 restraints weight = 3908.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.092293 restraints weight = 3772.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.092324 restraints weight = 3703.129| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.5954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3366 Z= 0.092 Angle : 0.462 8.159 4562 Z= 0.241 Chirality : 0.043 0.127 497 Planarity : 0.004 0.036 584 Dihedral : 4.839 42.977 459 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.47 % Allowed : 20.82 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.40), residues: 417 helix: -0.70 (0.38), residues: 179 sheet: -1.18 (0.71), residues: 56 loop : -1.67 (0.45), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 246 TYR 0.009 0.001 TYR A 132 PHE 0.011 0.001 PHE A 341 TRP 0.009 0.001 TRP A 63 HIS 0.001 0.000 HIS A 61 Details of bonding type rmsd covalent geometry : bond 0.00208 ( 3366) covalent geometry : angle 0.46155 ( 4562) hydrogen bonds : bond 0.03103 ( 120) hydrogen bonds : angle 4.18155 ( 348) *********************** 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 45 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.082 Fit side-chains REVERT: A 9 MET cc_start: 0.7990 (tpp) cc_final: 0.7781 (mmm) REVERT: A 90 MET cc_start: 0.8722 (tpt) cc_final: 0.8156 (tpt) REVERT: A 189 THR cc_start: 0.8058 (p) cc_final: 0.7512 (t) REVERT: A 388 HIS cc_start: 0.8177 (OUTLIER) cc_final: 0.7956 (t70) outliers start: 5 outliers final: 2 residues processed: 43 average time/residue: 0.0655 time to fit residues: 3.5179 Evaluate side-chains 36 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.121 ------------------------------------------------------------------------------- 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 388 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 29 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 28 optimal weight: 0.0770 chunk 11 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 22 optimal weight: 20.0000 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.122011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.091577 restraints weight = 5857.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.092315 restraints weight = 4611.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.092661 restraints weight = 3947.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.093212 restraints weight = 3632.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.093212 restraints weight = 3409.963| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.6291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 3366 Z= 0.090 Angle : 0.469 6.719 4562 Z= 0.244 Chirality : 0.043 0.128 497 Planarity : 0.004 0.036 584 Dihedral : 4.569 37.319 459 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.41), residues: 417 helix: -0.31 (0.38), residues: 185 sheet: -0.91 (0.73), residues: 56 loop : -1.71 (0.45), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 246 TYR 0.008 0.001 TYR A 132 PHE 0.010 0.001 PHE A 341 TRP 0.008 0.001 TRP A 63 HIS 0.003 0.000 HIS A 394 Details of bonding type rmsd covalent geometry : bond 0.00208 ( 3366) covalent geometry : angle 0.46935 ( 4562) hydrogen bonds : bond 0.02847 ( 120) hydrogen bonds : angle 4.08670 ( 348) *********************** 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 48 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.077 Fit side-chains REVERT: A 90 MET cc_start: 0.8738 (tpt) cc_final: 0.8150 (tpt) REVERT: A 232 LYS cc_start: 0.7920 (tppt) cc_final: 0.7717 (tmmt) REVERT: A 370 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.7306 (ttm110) REVERT: A 388 HIS cc_start: 0.8367 (OUTLIER) cc_final: 0.8011 (t70) outliers start: 8 outliers final: 3 residues processed: 47 average time/residue: 0.0573 time to fit residues: 3.3380 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 : 0.071 ------------------------------------------------------------------------------- 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 370 ARG Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 27 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 23 optimal weight: 30.0000 chunk 26 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 29 optimal weight: 0.0870 chunk 8 optimal weight: 3.9990 overall best weight: 1.5964 ------------------------------------------------------------------------------- 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 = 0.3493 r_free = 0.3493 target = 0.122098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.091712 restraints weight = 5846.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.092414 restraints weight = 4603.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.092985 restraints weight = 4007.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.093174 restraints weight = 3649.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.093174 restraints weight = 3470.344| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.6653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 3366 Z= 0.098 Angle : 0.465 6.394 4562 Z= 0.241 Chirality : 0.043 0.124 497 Planarity : 0.004 0.035 584 Dihedral : 4.440 34.037 459 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.93 % Allowed : 21.99 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.41), residues: 417 helix: 0.13 (0.39), residues: 179 sheet: -0.70 (0.75), residues: 56 loop : -1.46 (0.45), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 265 TYR 0.007 0.001 TYR A 132 PHE 0.011 0.001 PHE A 341 TRP 0.008 0.001 TRP A 63 HIS 0.006 0.001 HIS A 394 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 3366) covalent geometry : angle 0.46509 ( 4562) hydrogen bonds : bond 0.02863 ( 120) hydrogen bonds : angle 4.14659 ( 348) *********************** 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: 10 poor density : 40 time to evaluate : 0.140 Fit side-chains REVERT: A 90 MET cc_start: 0.8760 (tpt) cc_final: 0.8148 (tpt) REVERT: A 118 ARG cc_start: 0.7760 (mtp85) cc_final: 0.7470 (mpp80) REVERT: A 370 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7276 (ttm110) REVERT: A 388 HIS cc_start: 0.8404 (OUTLIER) cc_final: 0.7974 (t70) outliers start: 10 outliers final: 5 residues processed: 48 average time/residue: 0.0697 time to fit residues: 4.0559 Evaluate side-chains 44 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.115 ------------------------------------------------------------------------------- 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 307 ASP Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 370 ARG Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 417 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 12 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 3 optimal weight: 0.0370 chunk 24 optimal weight: 30.0000 chunk 33 optimal weight: 20.0000 chunk 29 optimal weight: 6.9990 chunk 26 optimal weight: 20.0000 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 overall best weight: 3.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN A 394 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.118084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.087676 restraints weight = 5982.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.088343 restraints weight = 4785.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.088757 restraints weight = 4134.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.088757 restraints weight = 3801.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.088757 restraints weight = 3801.978| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.7211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3366 Z= 0.160 Angle : 0.543 6.223 4562 Z= 0.282 Chirality : 0.046 0.163 497 Planarity : 0.004 0.035 584 Dihedral : 4.967 37.172 459 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.93 % Allowed : 22.29 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.41), residues: 417 helix: -0.10 (0.38), residues: 184 sheet: -1.01 (0.74), residues: 52 loop : -1.71 (0.45), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 58 TYR 0.006 0.001 TYR A 20 PHE 0.015 0.002 PHE A 341 TRP 0.009 0.001 TRP A 63 HIS 0.007 0.002 HIS A 394 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 3366) covalent geometry : angle 0.54280 ( 4562) hydrogen bonds : bond 0.03900 ( 120) hydrogen bonds : angle 4.39000 ( 348) *********************** 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 52 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.170 Fit side-chains REVERT: A 13 GLN cc_start: 0.8578 (mm-40) cc_final: 0.7963 (mt0) REVERT: A 118 ARG cc_start: 0.7833 (mtp85) cc_final: 0.7372 (mpp80) REVERT: A 232 LYS cc_start: 0.7740 (tppt) cc_final: 0.7528 (tmmt) REVERT: A 370 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7377 (ttm110) outliers start: 10 outliers final: 7 residues processed: 49 average time/residue: 0.0657 time to fit residues: 3.9115 Evaluate side-chains 48 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.148 ------------------------------------------------------------------------------- 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 173 VAL Chi-restraints excluded: chain A residue 280 THR 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 417 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 4 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 31 optimal weight: 20.0000 chunk 19 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 26 optimal weight: 20.0000 chunk 40 optimal weight: 0.9980 chunk 21 optimal weight: 30.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- 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 = 0.3419 r_free = 0.3419 target = 0.116683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.086443 restraints weight = 6003.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.087065 restraints weight = 4788.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.087609 restraints weight = 4143.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.088052 restraints weight = 3751.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.088114 restraints weight = 3507.619| |-----------------------------------------------------------------------------| r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.7535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 3366 Z= 0.188 Angle : 0.553 6.960 4562 Z= 0.288 Chirality : 0.047 0.161 497 Planarity : 0.004 0.034 584 Dihedral : 5.248 42.893 459 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.52 % Allowed : 21.41 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.40), residues: 417 helix: -0.36 (0.37), residues: 182 sheet: -1.30 (0.73), residues: 52 loop : -1.73 (0.45), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 122 TYR 0.008 0.001 TYR A 385 PHE 0.016 0.002 PHE A 341 TRP 0.009 0.001 TRP A 30 HIS 0.005 0.001 HIS A 394 Details of bonding type rmsd covalent geometry : bond 0.00459 ( 3366) covalent geometry : angle 0.55302 ( 4562) hydrogen bonds : bond 0.03966 ( 120) hydrogen bonds : angle 4.48676 ( 348) *********************** 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 53 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.121 Fit side-chains REVERT: A 118 ARG cc_start: 0.7841 (mtp85) cc_final: 0.7406 (mpp80) REVERT: A 370 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7351 (ttm110) REVERT: A 395 MET cc_start: 0.7990 (mmt) cc_final: 0.7696 (mmt) outliers start: 12 outliers final: 11 residues processed: 49 average time/residue: 0.0610 time to fit residues: 3.7143 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 : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 MET 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 307 ASP Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 370 ARG Chi-restraints excluded: chain A residue 382 TRP Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 417 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 0.0040 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 overall best weight: 1.1996 ------------------------------------------------------------------------------- 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 = 0.3474 r_free = 0.3474 target = 0.120802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.090816 restraints weight = 5912.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.091575 restraints weight = 4619.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.092146 restraints weight = 3970.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.092305 restraints weight = 3617.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.092305 restraints weight = 3457.740| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.7637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 3366 Z= 0.099 Angle : 0.522 8.031 4562 Z= 0.268 Chirality : 0.043 0.128 497 Planarity : 0.004 0.036 584 Dihedral : 4.747 39.374 459 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.64 % Allowed : 23.17 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.41), residues: 417 helix: 0.11 (0.38), residues: 182 sheet: -0.97 (0.75), residues: 52 loop : -1.61 (0.45), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 246 TYR 0.006 0.001 TYR A 132 PHE 0.010 0.001 PHE A 341 TRP 0.010 0.001 TRP A 63 HIS 0.006 0.001 HIS A 394 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 3366) covalent geometry : angle 0.52161 ( 4562) hydrogen bonds : bond 0.02931 ( 120) hydrogen bonds : angle 4.12598 ( 348) *********************** 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: 9 poor density : 42 time to evaluate : 0.124 Fit side-chains REVERT: A 370 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7265 (ttm110) outliers start: 9 outliers final: 7 residues processed: 48 average time/residue: 0.0710 time to fit residues: 4.1714 Evaluate side-chains 47 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 280 THR 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 388 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 13 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 22 optimal weight: 30.0000 chunk 24 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 28 optimal weight: 20.0000 chunk 18 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.118412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.087992 restraints weight = 5999.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.088688 restraints weight = 4789.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.088688 restraints weight = 4146.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 16)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.088688 restraints weight = 4145.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.088688 restraints weight = 4145.503| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.7777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3366 Z= 0.144 Angle : 0.523 6.283 4562 Z= 0.274 Chirality : 0.045 0.136 497 Planarity : 0.004 0.036 584 Dihedral : 4.908 41.415 459 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.41), residues: 417 helix: -0.01 (0.38), residues: 182 sheet: -1.05 (0.74), residues: 52 loop : -1.66 (0.46), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 122 TYR 0.005 0.001 TYR A 20 PHE 0.013 0.002 PHE A 341 TRP 0.010 0.001 TRP A 63 HIS 0.004 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 3366) covalent geometry : angle 0.52317 ( 4562) hydrogen bonds : bond 0.03431 ( 120) hydrogen bonds : angle 4.30103 ( 348) ********************** 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 : 0.137 Fit side-chains REVERT: A 13 GLN cc_start: 0.8502 (mm-40) cc_final: 0.7946 (mt0) REVERT: A 370 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.7335 (ttm110) outliers start: 10 outliers final: 8 residues processed: 48 average time/residue: 0.0640 time to fit residues: 3.8513 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 : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 280 THR 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 388 HIS Chi-restraints excluded: chain A residue 417 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 18 optimal weight: 0.0980 chunk 39 optimal weight: 6.9990 chunk 3 optimal weight: 0.0010 chunk 33 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 7 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- 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 = 0.122580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.092518 restraints weight = 5979.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.093261 restraints weight = 4769.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.093580 restraints weight = 4131.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.093580 restraints weight = 3806.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.093580 restraints weight = 3806.821| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.7933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3366 Z= 0.086 Angle : 0.488 6.133 4562 Z= 0.255 Chirality : 0.043 0.190 497 Planarity : 0.004 0.039 584 Dihedral : 4.464 35.912 459 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.35 % Allowed : 23.75 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.41), residues: 417 helix: 0.33 (0.38), residues: 183 sheet: -0.77 (0.76), residues: 52 loop : -1.57 (0.45), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 246 TYR 0.006 0.001 TYR A 132 PHE 0.007 0.001 PHE A 341 TRP 0.006 0.001 TRP A 89 HIS 0.001 0.000 HIS A 394 Details of bonding type rmsd covalent geometry : bond 0.00196 ( 3366) covalent geometry : angle 0.48763 ( 4562) hydrogen bonds : bond 0.02567 ( 120) hydrogen bonds : angle 3.87548 ( 348) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 677.45 seconds wall clock time: 12 minutes 20.43 seconds (740.43 seconds total)