Starting phenix.real_space_refine on Thu Jul 2 14:10:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eo4_19845/07_2026/9eo4_19845_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eo4_19845/07_2026/9eo4_19845.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9eo4_19845/07_2026/9eo4_19845_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eo4_19845/07_2026/9eo4_19845_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9eo4_19845/07_2026/9eo4_19845.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eo4_19845/07_2026/9eo4_19845.map" } resolution = 2.66 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= -0.001 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians S 23 5.16 5 Cl 1 4.86 5 Na 1 4.78 5 C 3001 2.51 5 N 685 2.21 5 O 748 1.98 5 H 4322 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8781 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 8634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 8634 Classifications: {'peptide': 546} Modifications used: {'ACID-ASP': 1, 'ACID-GLU': 1} Link IDs: {'PTRANS': 23, 'TRANS': 522} Chain breaks: 1 Chain: "B" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 145 Ad-hoc single atom residues: {' NA': 1, ' CL': 1} Unusual residues: {'CLR': 3, 'COC': 1, 'Y01': 1} Classifications: {'undetermined': 5, 'water': 4} Link IDs: {None: 7} Chain breaks: 2 Time building chain proxies: 1.63, per 1000 atoms: 0.19 Number of scatterers: 8781 At special positions: 0 Unit cell: (83.375, 66.7, 80.475, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 1 17.00 S 23 16.00 Na 1 11.00 O 748 8.00 N 685 7.00 C 3001 6.00 H 4322 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 189 " distance=2.03 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: 0.60 Conformation dependent library (CDL) restraints added in 261.9 milliseconds 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1004 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 1 sheets defined 82.8% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'B' and resid 65 through 78 removed outlier: 3.904A pdb=" N PHE B 69 " --> pdb=" O LYS B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 85 Processing helix chain 'B' and resid 85 through 93 Processing helix chain 'B' and resid 94 through 97 Processing helix chain 'B' and resid 98 through 109 Processing helix chain 'B' and resid 109 through 125 removed outlier: 3.543A pdb=" N LEU B 113 " --> pdb=" O ALA B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 138 Processing helix chain 'B' and resid 139 through 153 removed outlier: 3.800A pdb=" N PHE B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 169 removed outlier: 3.684A pdb=" N ILE B 159 " --> pdb=" O PHE B 155 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE B 160 " --> pdb=" O TYR B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 220 Processing helix chain 'B' and resid 223 through 227 removed outlier: 3.538A pdb=" N GLN B 226 " --> pdb=" O HIS B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 256 Processing helix chain 'B' and resid 258 through 270 removed outlier: 4.445A pdb=" N LYS B 264 " --> pdb=" O LYS B 260 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N TRP B 267 " --> pdb=" O GLY B 263 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ILE B 268 " --> pdb=" O LYS B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 286 removed outlier: 4.033A pdb=" N THR B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 299 Processing helix chain 'B' and resid 301 through 306 removed outlier: 3.588A pdb=" N CYS B 306 " --> pdb=" O TYR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 322 removed outlier: 3.834A pdb=" N TRP B 311 " --> pdb=" O GLU B 307 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU B 322 " --> pdb=" O VAL B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 334 Processing helix chain 'B' and resid 341 through 376 removed outlier: 3.693A pdb=" N GLY B 361 " --> pdb=" O SER B 357 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N PHE B 362 " --> pdb=" O PHE B 358 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL B 363 " --> pdb=" O SER B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 383 Processing helix chain 'B' and resid 388 through 400 removed outlier: 3.708A pdb=" N ILE B 393 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N TYR B 394 " --> pdb=" O ILE B 390 " (cutoff:3.500A) Proline residue: B 395 - end of helix removed outlier: 3.805A pdb=" N THR B 400 " --> pdb=" O GLU B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 438 removed outlier: 3.772A pdb=" N ASP B 421 " --> pdb=" O THR B 417 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 442 Processing helix chain 'B' and resid 444 through 460 removed outlier: 3.605A pdb=" N PHE B 448 " --> pdb=" O HIS B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 463 No H-bonds generated for 'chain 'B' and resid 461 through 463' Processing helix chain 'B' and resid 467 through 479 removed outlier: 3.801A pdb=" N VAL B 471 " --> pdb=" O GLY B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 497 removed outlier: 3.614A pdb=" N LEU B 485 " --> pdb=" O GLY B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 513 Processing helix chain 'B' and resid 517 through 526 Processing helix chain 'B' and resid 526 through 542 Processing helix chain 'B' and resid 554 through 570 removed outlier: 3.835A pdb=" N SER B 568 " --> pdb=" O ILE B 564 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N MET B 569 " --> pdb=" O ALA B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 583 Processing helix chain 'B' and resid 586 through 596 removed outlier: 3.561A pdb=" N LEU B 591 " --> pdb=" O PHE B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 599 No H-bonds generated for 'chain 'B' and resid 597 through 599' Processing helix chain 'B' and resid 600 through 607 Processing helix chain 'B' and resid 609 through 612 Processing helix chain 'B' and resid 613 through 619 removed outlier: 3.648A pdb=" N TRP B 617 " --> pdb=" O THR B 613 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 547 through 548 removed outlier: 3.639A pdb=" N TYR B 548 " --> pdb=" O TYR B 551 " (cutoff:3.500A) 282 hydrogen bonds defined for protein. 822 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: 1.44 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 4312 1.03 - 1.23: 45 1.23 - 1.43: 1925 1.43 - 1.62: 2606 1.62 - 1.82: 34 Bond restraints: 8922 Sorted by residual: bond pdb=" N ALA B 57 " pdb=" H ALA B 57 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" C LYS B 66 " pdb=" O LYS B 66 " ideal model delta sigma weight residual 1.236 1.172 0.064 1.29e-02 6.01e+03 2.43e+01 bond pdb=" C29 COC B 707 " pdb=" C8 COC B 707 " ideal model delta sigma weight residual 1.528 1.615 -0.087 2.00e-02 2.50e+03 1.89e+01 bond pdb=" C SER B 586 " pdb=" O SER B 586 " ideal model delta sigma weight residual 1.234 1.189 0.045 1.07e-02 8.73e+03 1.80e+01 bond pdb=" C SER B 568 " pdb=" O SER B 568 " ideal model delta sigma weight residual 1.236 1.188 0.049 1.16e-02 7.43e+03 1.78e+01 ... (remaining 8917 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 15923 2.47 - 4.94: 121 4.94 - 7.41: 9 7.41 - 9.88: 2 9.88 - 12.34: 2 Bond angle restraints: 16057 Sorted by residual: angle pdb=" CA SER B 568 " pdb=" C SER B 568 " pdb=" O SER B 568 " ideal model delta sigma weight residual 120.90 115.19 5.71 1.03e+00 9.43e-01 3.07e+01 angle pdb=" N SER B 568 " pdb=" CA SER B 568 " pdb=" C SER B 568 " ideal model delta sigma weight residual 111.03 105.21 5.82 1.11e+00 8.12e-01 2.75e+01 angle pdb=" CA SER B 586 " pdb=" C SER B 586 " pdb=" O SER B 586 " ideal model delta sigma weight residual 121.67 116.04 5.63 1.26e+00 6.30e-01 2.00e+01 angle pdb=" CA MET B 569 " pdb=" C MET B 569 " pdb=" O MET B 569 " ideal model delta sigma weight residual 120.10 115.18 4.92 1.13e+00 7.83e-01 1.90e+01 angle pdb=" N ARG B 588 " pdb=" CA ARG B 588 " pdb=" C ARG B 588 " ideal model delta sigma weight residual 112.90 107.33 5.57 1.31e+00 5.83e-01 1.81e+01 ... (remaining 16052 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.73: 4279 35.73 - 71.46: 164 71.46 - 107.19: 8 107.19 - 142.92: 1 142.92 - 178.64: 2 Dihedral angle restraints: 4454 sinusoidal: 2433 harmonic: 2021 Sorted by residual: dihedral pdb=" CD ARG B 443 " pdb=" NE ARG B 443 " pdb=" CZ ARG B 443 " pdb=" NH1 ARG B 443 " ideal model delta sinusoidal sigma weight residual 0.00 -78.07 78.07 1 1.00e+01 1.00e-02 7.62e+01 dihedral pdb=" CB ASP B 421 " pdb=" CG ASP B 421 " pdb=" OD2 ASP B 421 " pdb=" HD2 ASP B 421 " ideal model delta harmonic sigma weight residual -180.00 -1.36 -178.64 0 3.00e+01 1.11e-03 3.55e+01 dihedral pdb=" CG GLU B 491 " pdb=" CD GLU B 491 " pdb=" OE2 GLU B 491 " pdb=" HE2 GLU B 491 " ideal model delta harmonic sigma weight residual 180.00 1.54 178.46 0 3.00e+01 1.11e-03 3.54e+01 ... (remaining 4451 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 616 0.057 - 0.113: 96 0.113 - 0.170: 8 0.170 - 0.226: 0 0.226 - 0.283: 2 Chirality restraints: 722 Sorted by residual: chirality pdb=" C8 COC B 707 " pdb=" C10 COC B 707 " pdb=" C29 COC B 707 " pdb=" C6 COC B 707 " both_signs ideal model delta sigma weight residual False 2.53 2.81 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" C29 COC B 707 " pdb=" C26 COC B 707 " pdb=" C8 COC B 707 " pdb=" O1 COC B 707 " both_signs ideal model delta sigma weight residual False -2.38 -2.64 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA ILE B 67 " pdb=" N ILE B 67 " pdb=" C ILE B 67 " pdb=" CB ILE B 67 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.05e-01 ... (remaining 719 not shown) Planarity restraints: 1271 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 443 " 1.080 9.50e-02 1.11e+02 5.49e-01 3.98e+03 pdb=" NE ARG B 443 " -0.081 2.00e-02 2.50e+03 pdb=" CZ ARG B 443 " -0.037 2.00e-02 2.50e+03 pdb=" NH1 ARG B 443 " 0.059 2.00e-02 2.50e+03 pdb=" NH2 ARG B 443 " -0.056 2.00e-02 2.50e+03 pdb="HH11 ARG B 443 " 0.729 2.00e-02 2.50e+03 pdb="HH12 ARG B 443 " -0.540 2.00e-02 2.50e+03 pdb="HH21 ARG B 443 " 0.529 2.00e-02 2.50e+03 pdb="HH22 ARG B 443 " -0.651 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 85 " -0.271 9.50e-02 1.11e+02 4.20e-01 3.79e+03 pdb=" NE ARG B 85 " 0.326 2.00e-02 2.50e+03 pdb=" CZ ARG B 85 " 0.087 2.00e-02 2.50e+03 pdb=" NH1 ARG B 85 " -0.058 2.00e-02 2.50e+03 pdb=" NH2 ARG B 85 " -0.019 2.00e-02 2.50e+03 pdb="HH11 ARG B 85 " 0.632 2.00e-02 2.50e+03 pdb="HH12 ARG B 85 " -0.842 2.00e-02 2.50e+03 pdb="HH21 ARG B 85 " -0.429 2.00e-02 2.50e+03 pdb="HH22 ARG B 85 " 0.316 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 317 " 0.125 2.00e-02 2.50e+03 1.31e-01 2.59e+02 pdb=" CD GLN B 317 " -0.013 2.00e-02 2.50e+03 pdb=" OE1 GLN B 317 " -0.114 2.00e-02 2.50e+03 pdb=" NE2 GLN B 317 " -0.004 2.00e-02 2.50e+03 pdb="HE21 GLN B 317 " 0.197 2.00e-02 2.50e+03 pdb="HE22 GLN B 317 " -0.190 2.00e-02 2.50e+03 ... (remaining 1268 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 727 2.22 - 2.82: 18833 2.82 - 3.41: 25416 3.41 - 4.01: 34022 4.01 - 4.60: 52869 Nonbonded interactions: 131867 Sorted by model distance: nonbonded pdb=" HH TYR B 499 " pdb=" OD2 ASP B 507 " model vdw 1.628 2.450 nonbonded pdb="HH22 ARG B 125 " pdb=" O ASN B 336 " model vdw 1.642 2.450 nonbonded pdb=" O GLN B 611 " pdb=" HE1 TRP B 617 " model vdw 1.647 2.450 nonbonded pdb=" OE2 GLU B 428 " pdb="HH22 ARG B 445 " model vdw 1.667 2.450 nonbonded pdb=" O VAL B 107 " pdb=" HH TYR B 519 " model vdw 1.695 2.450 ... (remaining 131862 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.410 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: 0.050 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.230 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 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 0.087 4601 Z= 0.325 Angle : 0.720 12.345 6302 Z= 0.419 Chirality : 0.041 0.283 722 Planarity : 0.022 0.488 750 Dihedral : 15.975 123.651 1808 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.87 % Allowed : 14.63 % Favored : 84.50 % 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: 1.45 (0.38), residues: 542 helix: 1.09 (0.27), residues: 377 sheet: None (None), residues: 0 loop : 0.99 (0.55), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 615 TYR 0.007 0.001 TYR B 575 PHE 0.013 0.001 PHE B 365 TRP 0.008 0.001 TRP B 238 HIS 0.002 0.000 HIS B 616 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.33 ( 4600) covalent geometry : angle 0.71909 / 0.42 ( 6300) SS BOND : bond 0.00075 / 0.04 ( 1) SS BOND : angle 1.59848 / 1.07 ( 2) hydrogen bonds : bond 0.12818 / 8.36 ( 282) hydrogen bonds : angle 6.07813 / 4.29 ( 822) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: B 174 GLU cc_start: 0.7159 (tt0) cc_final: 0.6793 (pt0) REVERT: B 239 GLN cc_start: 0.7865 (mp10) cc_final: 0.7628 (mt0) REVERT: B 295 ARG cc_start: 0.7225 (ttm-80) cc_final: 0.6746 (mtm-85) REVERT: B 360 SER cc_start: 0.8702 (m) cc_final: 0.8474 (p) REVERT: B 483 SER cc_start: 0.8544 (OUTLIER) cc_final: 0.8292 (p) REVERT: B 544 ARG cc_start: 0.6954 (mtm-85) cc_final: 0.6689 (mtm-85) outliers start: 4 outliers final: 3 residues processed: 76 average time/residue: 0.8358 time to fit residues: 66.6814 Evaluate side-chains 67 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 568 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.3980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 226 GLN B 444 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.114418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.094413 restraints weight = 15060.704| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.63 r_work: 0.2913 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4601 Z= 0.131 Angle : 0.501 4.475 6302 Z= 0.260 Chirality : 0.036 0.125 722 Planarity : 0.008 0.159 750 Dihedral : 7.719 59.469 891 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 1.31 % Allowed : 14.19 % Favored : 84.50 % 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: 1.50 (0.38), residues: 542 helix: 1.17 (0.27), residues: 395 sheet: None (None), residues: 0 loop : 0.82 (0.59), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 443 TYR 0.010 0.001 TYR B 252 PHE 0.014 0.001 PHE B 365 TRP 0.008 0.001 TRP B 238 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 4600) covalent geometry : angle 0.50065 / 0.26 ( 6300) SS BOND : bond 0.00081 / 0.04 ( 1) SS BOND : angle 1.69656 / 1.13 ( 2) hydrogen bonds : bond 0.04226 / 2.90 ( 282) hydrogen bonds : angle 4.61343 / 3.21 ( 822) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: B 174 GLU cc_start: 0.7687 (tt0) cc_final: 0.7468 (pt0) REVERT: B 295 ARG cc_start: 0.7648 (ttm-80) cc_final: 0.7168 (mtp180) REVERT: B 544 ARG cc_start: 0.7198 (mtm-85) cc_final: 0.6937 (mtm-85) outliers start: 6 outliers final: 3 residues processed: 66 average time/residue: 0.7039 time to fit residues: 48.9991 Evaluate side-chains 61 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 568 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 40 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.111918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.091622 restraints weight = 15196.538| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 1.62 r_work: 0.2892 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4601 Z= 0.159 Angle : 0.495 4.491 6302 Z= 0.259 Chirality : 0.036 0.132 722 Planarity : 0.005 0.051 750 Dihedral : 7.408 59.088 889 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.66 % Allowed : 14.85 % Favored : 84.50 % 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: 1.42 (0.37), residues: 542 helix: 1.17 (0.26), residues: 394 sheet: None (None), residues: 0 loop : 0.61 (0.58), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 615 TYR 0.010 0.001 TYR B 252 PHE 0.014 0.001 PHE B 365 TRP 0.008 0.001 TRP B 132 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 4600) covalent geometry : angle 0.49352 / 0.26 ( 6300) SS BOND : bond 0.00075 / 0.04 ( 1) SS BOND : angle 2.16035 / 1.44 ( 2) hydrogen bonds : bond 0.04259 / 2.94 ( 282) hydrogen bonds : angle 4.49883 / 3.13 ( 822) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.177 Fit side-chains revert: symmetry clash REVERT: B 174 GLU cc_start: 0.7767 (tt0) cc_final: 0.7506 (pt0) REVERT: B 295 ARG cc_start: 0.7656 (ttm-80) cc_final: 0.7140 (mtp180) REVERT: B 544 ARG cc_start: 0.7221 (mtm-85) cc_final: 0.6946 (mtm-85) outliers start: 3 outliers final: 3 residues processed: 59 average time/residue: 0.8844 time to fit residues: 54.7263 Evaluate side-chains 59 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 568 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 17 optimal weight: 0.3980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.116962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.096974 restraints weight = 15195.629| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.60 r_work: 0.2931 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4601 Z= 0.135 Angle : 0.475 4.445 6302 Z= 0.249 Chirality : 0.036 0.128 722 Planarity : 0.005 0.057 750 Dihedral : 7.094 58.491 889 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 0.66 % Allowed : 15.50 % Favored : 83.84 % 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: 1.50 (0.37), residues: 542 helix: 1.24 (0.26), residues: 394 sheet: None (None), residues: 0 loop : 0.59 (0.57), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 615 TYR 0.009 0.001 TYR B 252 PHE 0.014 0.001 PHE B 365 TRP 0.008 0.001 TRP B 238 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 4600) covalent geometry : angle 0.47346 / 0.25 ( 6300) SS BOND : bond 0.00110 / 0.06 ( 1) SS BOND : angle 1.88028 / 1.25 ( 2) hydrogen bonds : bond 0.03997 / 2.77 ( 282) hydrogen bonds : angle 4.36424 / 3.04 ( 822) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 174 GLU cc_start: 0.7759 (tt0) cc_final: 0.7542 (pt0) REVERT: B 295 ARG cc_start: 0.7677 (ttm-80) cc_final: 0.7162 (mtp180) REVERT: B 544 ARG cc_start: 0.7196 (mtm-85) cc_final: 0.6930 (mtm-85) outliers start: 3 outliers final: 3 residues processed: 57 average time/residue: 0.8521 time to fit residues: 50.9078 Evaluate side-chains 56 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 568 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 19 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 30 optimal weight: 0.0980 chunk 1 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.117215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.097394 restraints weight = 14999.626| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 1.59 r_work: 0.2939 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4601 Z= 0.124 Angle : 0.463 4.440 6302 Z= 0.243 Chirality : 0.035 0.128 722 Planarity : 0.004 0.060 750 Dihedral : 6.944 58.340 889 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.87 % Allowed : 15.07 % Favored : 84.06 % 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: 1.56 (0.37), residues: 542 helix: 1.30 (0.26), residues: 394 sheet: None (None), residues: 0 loop : 0.57 (0.56), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 615 TYR 0.009 0.001 TYR B 252 PHE 0.013 0.001 PHE B 365 TRP 0.008 0.001 TRP B 238 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 ( 4600) covalent geometry : angle 0.46192 / 0.24 ( 6300) SS BOND : bond 0.00087 / 0.05 ( 1) SS BOND : angle 1.80295 / 1.20 ( 2) hydrogen bonds : bond 0.03907 / 2.72 ( 282) hydrogen bonds : angle 4.30861 / 3.00 ( 822) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 174 GLU cc_start: 0.7768 (tt0) cc_final: 0.7511 (pt0) REVERT: B 295 ARG cc_start: 0.7684 (ttm-80) cc_final: 0.7164 (mtp180) REVERT: B 544 ARG cc_start: 0.7197 (mtm-85) cc_final: 0.6926 (mtm-85) outliers start: 4 outliers final: 2 residues processed: 59 average time/residue: 0.9861 time to fit residues: 60.7836 Evaluate side-chains 59 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 429 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.116535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.096638 restraints weight = 14937.081| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.59 r_work: 0.2899 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4601 Z= 0.151 Angle : 0.479 4.476 6302 Z= 0.252 Chirality : 0.036 0.130 722 Planarity : 0.005 0.071 750 Dihedral : 7.021 59.078 888 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 0.44 % Allowed : 15.72 % Favored : 83.84 % 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: 1.47 (0.37), residues: 542 helix: 1.26 (0.26), residues: 394 sheet: None (None), residues: 0 loop : 0.47 (0.56), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 615 TYR 0.010 0.001 TYR B 252 PHE 0.014 0.001 PHE B 365 TRP 0.008 0.001 TRP B 132 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 ( 4600) covalent geometry : angle 0.47775 / 0.25 ( 6300) SS BOND : bond 0.00089 / 0.05 ( 1) SS BOND : angle 2.07649 / 1.38 ( 2) hydrogen bonds : bond 0.03997 / 2.77 ( 282) hydrogen bonds : angle 4.33507 / 3.02 ( 822) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 174 GLU cc_start: 0.7750 (tt0) cc_final: 0.7413 (pt0) REVERT: B 226 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8099 (mt0) REVERT: B 295 ARG cc_start: 0.7590 (ttm-80) cc_final: 0.7296 (mtm-85) REVERT: B 544 ARG cc_start: 0.7148 (mtm-85) cc_final: 0.6847 (mtm-85) outliers start: 2 outliers final: 1 residues processed: 58 average time/residue: 1.0016 time to fit residues: 60.6325 Evaluate side-chains 57 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 55 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 226 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.117079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.097174 restraints weight = 15097.065| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.59 r_work: 0.2961 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4601 Z= 0.136 Angle : 0.468 4.446 6302 Z= 0.247 Chirality : 0.036 0.128 722 Planarity : 0.005 0.072 750 Dihedral : 6.898 59.672 888 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.87 % Allowed : 15.28 % Favored : 83.84 % 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 (0.37), residues: 542 helix: 1.28 (0.26), residues: 394 sheet: None (None), residues: 0 loop : 0.53 (0.56), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 615 TYR 0.009 0.001 TYR B 252 PHE 0.014 0.001 PHE B 365 TRP 0.008 0.001 TRP B 132 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 4600) covalent geometry : angle 0.46732 / 0.25 ( 6300) SS BOND : bond 0.00104 / 0.05 ( 1) SS BOND : angle 1.90461 / 1.27 ( 2) hydrogen bonds : bond 0.03893 / 2.70 ( 282) hydrogen bonds : angle 4.29909 / 2.99 ( 822) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 174 GLU cc_start: 0.7803 (tt0) cc_final: 0.7525 (pt0) REVERT: B 295 ARG cc_start: 0.7685 (ttm-80) cc_final: 0.7410 (mtm-85) REVERT: B 544 ARG cc_start: 0.7228 (mtm-85) cc_final: 0.6946 (mtm-85) outliers start: 4 outliers final: 2 residues processed: 59 average time/residue: 1.0383 time to fit residues: 64.0346 Evaluate side-chains 57 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 55 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 429 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 0.9990 chunk 8 optimal weight: 0.0770 chunk 34 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 37 optimal weight: 0.0000 chunk 29 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 16 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 overall best weight: 0.4142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.118414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.098682 restraints weight = 14959.921| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.58 r_work: 0.2989 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4601 Z= 0.103 Angle : 0.446 4.397 6302 Z= 0.235 Chirality : 0.035 0.127 722 Planarity : 0.005 0.076 750 Dihedral : 6.584 58.436 888 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 0.44 % Allowed : 15.94 % Favored : 83.62 % 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: 1.55 (0.37), residues: 542 helix: 1.34 (0.27), residues: 397 sheet: None (None), residues: 0 loop : 0.37 (0.55), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 615 TYR 0.008 0.001 TYR B 252 PHE 0.013 0.001 PHE B 365 TRP 0.008 0.001 TRP B 238 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 ( 4600) covalent geometry : angle 0.44565 / 0.23 ( 6300) SS BOND : bond 0.00074 / 0.04 ( 1) SS BOND : angle 1.51760 / 1.01 ( 2) hydrogen bonds : bond 0.03675 / 2.57 ( 282) hydrogen bonds : angle 4.20492 / 2.93 ( 822) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 174 GLU cc_start: 0.7786 (tt0) cc_final: 0.7541 (pt0) REVERT: B 295 ARG cc_start: 0.7680 (ttm-80) cc_final: 0.7152 (mtp180) REVERT: B 514 GLN cc_start: 0.7950 (pp30) cc_final: 0.7404 (pt0) REVERT: B 544 ARG cc_start: 0.7193 (mtm-85) cc_final: 0.6908 (mtm-85) outliers start: 2 outliers final: 2 residues processed: 56 average time/residue: 0.9491 time to fit residues: 55.7512 Evaluate side-chains 56 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 429 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 34 optimal weight: 0.3980 chunk 28 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.117488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.097673 restraints weight = 15049.964| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.58 r_work: 0.2974 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4601 Z= 0.131 Angle : 0.462 4.461 6302 Z= 0.242 Chirality : 0.036 0.128 722 Planarity : 0.005 0.079 750 Dihedral : 6.735 58.163 888 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.44 % Allowed : 15.50 % Favored : 84.06 % 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: 1.49 (0.37), residues: 542 helix: 1.31 (0.26), residues: 397 sheet: None (None), residues: 0 loop : 0.32 (0.55), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 615 TYR 0.009 0.001 TYR B 252 PHE 0.014 0.001 PHE B 365 TRP 0.008 0.001 TRP B 132 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 4600) covalent geometry : angle 0.46123 / 0.24 ( 6300) SS BOND : bond 0.00074 / 0.04 ( 1) SS BOND : angle 1.80900 / 1.21 ( 2) hydrogen bonds : bond 0.03808 / 2.66 ( 282) hydrogen bonds : angle 4.23159 / 2.95 ( 822) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 55 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 174 GLU cc_start: 0.7788 (tt0) cc_final: 0.7467 (pt0) REVERT: B 295 ARG cc_start: 0.7690 (ttm-80) cc_final: 0.7161 (mtp180) REVERT: B 544 ARG cc_start: 0.7197 (mtm-85) cc_final: 0.6911 (mtm-85) outliers start: 2 outliers final: 2 residues processed: 57 average time/residue: 0.9440 time to fit residues: 56.4379 Evaluate side-chains 57 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 55 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 429 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 42 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 44 optimal weight: 0.3980 chunk 34 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 0.4980 chunk 46 optimal weight: 0.5980 chunk 32 optimal weight: 0.0980 chunk 36 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.118120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.098450 restraints weight = 15021.840| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.58 r_work: 0.2988 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4601 Z= 0.111 Angle : 0.449 4.409 6302 Z= 0.236 Chirality : 0.035 0.146 722 Planarity : 0.004 0.035 750 Dihedral : 6.567 57.236 888 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 0.44 % Allowed : 15.72 % Favored : 83.84 % 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: 1.57 (0.37), residues: 542 helix: 1.37 (0.26), residues: 397 sheet: None (None), residues: 0 loop : 0.37 (0.55), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 615 TYR 0.008 0.001 TYR B 252 PHE 0.013 0.001 PHE B 365 TRP 0.008 0.001 TRP B 238 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 4600) covalent geometry : angle 0.44795 / 0.24 ( 6300) SS BOND : bond 0.00090 / 0.05 ( 1) SS BOND : angle 1.60923 / 1.07 ( 2) hydrogen bonds : bond 0.03693 / 2.58 ( 282) hydrogen bonds : angle 4.19102 / 2.92 ( 822) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 55 time to evaluate : 0.145 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 174 GLU cc_start: 0.7769 (tt0) cc_final: 0.7483 (pt0) REVERT: B 295 ARG cc_start: 0.7686 (ttm-80) cc_final: 0.7159 (mtp180) REVERT: B 514 GLN cc_start: 0.7956 (pp30) cc_final: 0.7408 (pt0) REVERT: B 544 ARG cc_start: 0.7165 (mtm-85) cc_final: 0.6838 (mtm-85) outliers start: 2 outliers final: 2 residues processed: 57 average time/residue: 0.9321 time to fit residues: 55.7228 Evaluate side-chains 57 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 55 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 429 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 31 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 52 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.117956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.098261 restraints weight = 14964.678| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.57 r_work: 0.2983 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4601 Z= 0.121 Angle : 0.456 4.439 6302 Z= 0.239 Chirality : 0.035 0.128 722 Planarity : 0.005 0.092 750 Dihedral : 6.611 57.012 888 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.66 % Allowed : 15.28 % Favored : 84.06 % 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: 1.56 (0.37), residues: 542 helix: 1.36 (0.26), residues: 397 sheet: None (None), residues: 0 loop : 0.35 (0.55), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 615 TYR 0.008 0.001 TYR B 252 PHE 0.013 0.001 PHE B 365 TRP 0.008 0.001 TRP B 238 HIS 0.002 0.001 HIS B 616 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 4600) covalent geometry : angle 0.45496 / 0.24 ( 6300) SS BOND : bond 0.00065 / 0.03 ( 1) SS BOND : angle 1.70629 / 1.14 ( 2) hydrogen bonds : bond 0.03729 / 2.60 ( 282) hydrogen bonds : angle 4.19270 / 2.92 ( 822) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2908.80 seconds wall clock time: 49 minutes 57.36 seconds (2997.36 seconds total)