Starting phenix.real_space_refine on Wed Mar 5 22:03:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kdn_37140/03_2025/8kdn_37140.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kdn_37140/03_2025/8kdn_37140.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kdn_37140/03_2025/8kdn_37140.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kdn_37140/03_2025/8kdn_37140.map" model { file = "/net/cci-nas-00/data/ceres_data/8kdn_37140/03_2025/8kdn_37140.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kdn_37140/03_2025/8kdn_37140.cif" } resolution = 4.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.010 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 22 5.16 5 C 2635 2.51 5 N 615 2.21 5 O 658 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3930 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 409 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "B" Number of atoms: 3509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3509 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 23, 'TRANS': 430} Chain breaks: 1 Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 2.92, per 1000 atoms: 0.74 Number of scatterers: 3930 At special positions: 0 Unit cell: (76.725, 85.932, 79.794, 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 22 16.00 O 658 8.00 N 615 7.00 C 2635 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 210 " - pdb=" SG CYS B 164 " distance=2.11 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: 1.00 Conformation dependent library (CDL) restraints added in 497.3 milliseconds 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 934 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 0 sheets defined 86.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 165 through 173 removed outlier: 4.327A pdb=" N LYS A 171 " --> pdb=" O GLU A 167 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N VAL A 172 " --> pdb=" O GLU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 207 removed outlier: 4.001A pdb=" N TRP A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 65 removed outlier: 3.685A pdb=" N ILE B 59 " --> pdb=" O GLY B 55 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLY B 65 " --> pdb=" O GLY B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 71 Processing helix chain 'B' and resid 72 through 80 removed outlier: 4.397A pdb=" N GLU B 78 " --> pdb=" O GLY B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 110 removed outlier: 3.907A pdb=" N GLY B 93 " --> pdb=" O TRP B 89 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU B 106 " --> pdb=" O CYS B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 125 removed outlier: 3.663A pdb=" N VAL B 123 " --> pdb=" O TYR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 139 removed outlier: 3.581A pdb=" N LYS B 132 " --> pdb=" O PRO B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 157 removed outlier: 3.616A pdb=" N VAL B 148 " --> pdb=" O SER B 144 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR B 155 " --> pdb=" O VAL B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 161 Processing helix chain 'B' and resid 167 through 188 Processing helix chain 'B' and resid 189 through 221 Processing helix chain 'B' and resid 239 through 255 removed outlier: 4.510A pdb=" N LEU B 245 " --> pdb=" O GLY B 241 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY B 250 " --> pdb=" O ALA B 246 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ALA B 253 " --> pdb=" O SER B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 267 removed outlier: 4.192A pdb=" N LEU B 260 " --> pdb=" O TRP B 257 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASN B 261 " --> pdb=" O ASN B 258 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR B 264 " --> pdb=" O ASN B 261 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N GLU B 265 " --> pdb=" O PHE B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 300 Proline residue: B 275 - end of helix Proline residue: B 283 - end of helix removed outlier: 3.594A pdb=" N PHE B 297 " --> pdb=" O ASN B 293 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 308 Processing helix chain 'B' and resid 310 through 320 Processing helix chain 'B' and resid 325 through 356 removed outlier: 3.563A pdb=" N ARG B 348 " --> pdb=" O PHE B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 365 removed outlier: 3.531A pdb=" N LEU B 363 " --> pdb=" O PRO B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 387 removed outlier: 3.578A pdb=" N LEU B 377 " --> pdb=" O PRO B 373 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N TYR B 387 " --> pdb=" O MET B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 390 No H-bonds generated for 'chain 'B' and resid 388 through 390' Processing helix chain 'B' and resid 393 through 422 removed outlier: 3.838A pdb=" N ILE B 397 " --> pdb=" O ILE B 393 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N PHE B 402 " --> pdb=" O ASN B 398 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE B 403 " --> pdb=" O PHE B 399 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN B 404 " --> pdb=" O PHE B 400 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N TRP B 405 " --> pdb=" O SER B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 454 removed outlier: 3.874A pdb=" N LEU B 441 " --> pdb=" O VAL B 437 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER B 450 " --> pdb=" O LEU B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 467 removed outlier: 3.550A pdb=" N THR B 463 " --> pdb=" O GLY B 459 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER B 467 " --> pdb=" O THR B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 476 removed outlier: 4.145A pdb=" N VAL B 471 " --> pdb=" O SER B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 501 removed outlier: 3.707A pdb=" N GLY B 488 " --> pdb=" O TRP B 484 " (cutoff:3.500A) 292 hydrogen bonds defined for protein. 852 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: 1.03 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 664 1.33 - 1.45: 1057 1.45 - 1.58: 2279 1.58 - 1.70: 2 1.70 - 1.82: 31 Bond restraints: 4033 Sorted by residual: bond pdb=" CB SER B 338 " pdb=" OG SER B 338 " ideal model delta sigma weight residual 1.417 1.488 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" C VAL B 166 " pdb=" N PRO B 167 " ideal model delta sigma weight residual 1.332 1.365 -0.033 1.12e-02 7.97e+03 8.50e+00 bond pdb=" C SER B 143 " pdb=" O SER B 143 " ideal model delta sigma weight residual 1.237 1.203 0.034 1.19e-02 7.06e+03 8.12e+00 bond pdb=" CA LEU B 274 " pdb=" C LEU B 274 " ideal model delta sigma weight residual 1.521 1.551 -0.030 1.08e-02 8.57e+03 7.71e+00 bond pdb=" C LEU B 180 " pdb=" O LEU B 180 " ideal model delta sigma weight residual 1.237 1.205 0.031 1.16e-02 7.43e+03 7.35e+00 ... (remaining 4028 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 4131 1.78 - 3.56: 1131 3.56 - 5.34: 207 5.34 - 7.11: 32 7.11 - 8.89: 4 Bond angle restraints: 5505 Sorted by residual: angle pdb=" CA ASP B 116 " pdb=" CB ASP B 116 " pdb=" CG ASP B 116 " ideal model delta sigma weight residual 112.60 118.63 -6.03 1.00e+00 1.00e+00 3.64e+01 angle pdb=" CA PHE B 200 " pdb=" CB PHE B 200 " pdb=" CG PHE B 200 " ideal model delta sigma weight residual 113.80 107.96 5.84 1.00e+00 1.00e+00 3.41e+01 angle pdb=" C PHE B 389 " pdb=" CA PHE B 389 " pdb=" CB PHE B 389 " ideal model delta sigma weight residual 111.74 119.36 -7.62 1.37e+00 5.33e-01 3.09e+01 angle pdb=" CA PHE B 445 " pdb=" CB PHE B 445 " pdb=" CG PHE B 445 " ideal model delta sigma weight residual 113.80 119.22 -5.42 1.00e+00 1.00e+00 2.94e+01 angle pdb=" N TYR B 259 " pdb=" CA TYR B 259 " pdb=" C TYR B 259 " ideal model delta sigma weight residual 111.36 116.60 -5.24 1.09e+00 8.42e-01 2.31e+01 ... (remaining 5500 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 2151 17.97 - 35.94: 151 35.94 - 53.91: 20 53.91 - 71.88: 3 71.88 - 89.85: 4 Dihedral angle restraints: 2329 sinusoidal: 876 harmonic: 1453 Sorted by residual: dihedral pdb=" CA PRO B 455 " pdb=" C PRO B 455 " pdb=" N VAL B 456 " pdb=" CA VAL B 456 " ideal model delta harmonic sigma weight residual 180.00 -150.56 -29.44 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA TRP B 477 " pdb=" C TRP B 477 " pdb=" N TRP B 478 " pdb=" CA TRP B 478 " ideal model delta harmonic sigma weight residual -180.00 -152.28 -27.72 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA ILE B 139 " pdb=" C ILE B 139 " pdb=" N ILE B 140 " pdb=" CA ILE B 140 " ideal model delta harmonic sigma weight residual -180.00 -154.56 -25.44 0 5.00e+00 4.00e-02 2.59e+01 ... (remaining 2326 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 430 0.072 - 0.145: 173 0.145 - 0.217: 51 0.217 - 0.290: 10 0.290 - 0.362: 1 Chirality restraints: 665 Sorted by residual: chirality pdb=" CA SER B 113 " pdb=" N SER B 113 " pdb=" C SER B 113 " pdb=" CB SER B 113 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.27e+00 chirality pdb=" CB ILE B 147 " pdb=" CA ILE B 147 " pdb=" CG1 ILE B 147 " pdb=" CG2 ILE B 147 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA THR B 194 " pdb=" N THR B 194 " pdb=" C THR B 194 " pdb=" CB THR B 194 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 662 not shown) Planarity restraints: 660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 141 " 0.316 9.50e-02 1.11e+02 1.42e-01 1.27e+01 pdb=" NE ARG B 141 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG B 141 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG B 141 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B 141 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 348 " 0.314 9.50e-02 1.11e+02 1.41e-01 1.22e+01 pdb=" NE ARG B 348 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG B 348 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG B 348 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B 348 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 182 " 0.269 9.50e-02 1.11e+02 1.21e-01 9.11e+00 pdb=" NE ARG A 182 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A 182 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 182 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A 182 " 0.012 2.00e-02 2.50e+03 ... (remaining 657 not shown) Histogram of nonbonded interaction distances: 2.61 - 3.07: 2508 3.07 - 3.53: 4300 3.53 - 3.98: 6293 3.98 - 4.44: 7251 4.44 - 4.90: 11235 Nonbonded interactions: 31587 Sorted by model distance: nonbonded pdb=" O VAL B 288 " pdb=" OG1 THR B 292 " model vdw 2.610 3.040 nonbonded pdb=" OH TYR B 103 " pdb=" OD1 ASP B 116 " model vdw 2.614 3.040 nonbonded pdb=" NH2 ARG A 182 " pdb=" O LYS B 498 " model vdw 2.633 3.120 nonbonded pdb=" OG SER B 395 " pdb=" OE1 GLU B 457 " model vdw 2.635 3.040 nonbonded pdb=" O ALA B 295 " pdb=" OG1 THR B 298 " model vdw 2.635 3.040 ... (remaining 31582 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.300 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6349 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 : 0.011 0.071 4033 Z= 0.710 Angle : 1.680 8.893 5505 Z= 1.133 Chirality : 0.084 0.362 665 Planarity : 0.012 0.142 660 Dihedral : 13.038 89.853 1392 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 0.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.17 % Allowed : 4.45 % Favored : 94.38 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.31), residues: 500 helix: -1.67 (0.21), residues: 378 sheet: None (None), residues: 0 loop : -1.70 (0.58), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRP B 257 HIS 0.004 0.001 HIS B 367 PHE 0.024 0.005 PHE B 69 TYR 0.021 0.005 TYR B 146 ARG 0.011 0.001 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 169 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 VAL cc_start: 0.7315 (t) cc_final: 0.7075 (p) REVERT: B 111 SER cc_start: 0.8071 (p) cc_final: 0.7536 (m) REVERT: B 141 ARG cc_start: 0.6753 (tpp-160) cc_final: 0.6444 (tpp-160) REVERT: B 239 ASP cc_start: 0.6811 (t0) cc_final: 0.6364 (t0) REVERT: B 249 SER cc_start: 0.8405 (m) cc_final: 0.8157 (p) REVERT: B 272 ARG cc_start: 0.5694 (ttt180) cc_final: 0.5404 (tpt170) REVERT: B 297 PHE cc_start: 0.7492 (m-80) cc_final: 0.7155 (m-80) REVERT: B 298 THR cc_start: 0.8119 (p) cc_final: 0.7838 (p) REVERT: B 315 PHE cc_start: 0.8096 (t80) cc_final: 0.7843 (t80) REVERT: B 318 TYR cc_start: 0.9131 (t80) cc_final: 0.8884 (t80) REVERT: B 319 HIS cc_start: 0.6702 (m-70) cc_final: 0.5654 (m-70) REVERT: B 365 MET cc_start: 0.8073 (mmt) cc_final: 0.7718 (mmt) REVERT: B 367 HIS cc_start: 0.7775 (t-90) cc_final: 0.7168 (t-90) REVERT: B 369 GLN cc_start: 0.8257 (mm-40) cc_final: 0.8028 (mp10) REVERT: B 391 LYS cc_start: 0.7614 (tptm) cc_final: 0.7241 (mmtt) REVERT: B 394 PHE cc_start: 0.6433 (t80) cc_final: 0.6163 (t80) REVERT: B 500 MET cc_start: 0.5676 (mmt) cc_final: 0.4931 (mtm) outliers start: 5 outliers final: 1 residues processed: 170 average time/residue: 0.1444 time to fit residues: 30.5637 Evaluate side-chains 116 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 115 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 0.4980 chunk 15 optimal weight: 0.8980 chunk 23 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.122520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.099038 restraints weight = 6332.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.102334 restraints weight = 3601.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.104479 restraints weight = 2501.796| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4033 Z= 0.185 Angle : 0.646 6.619 5505 Z= 0.332 Chirality : 0.043 0.179 665 Planarity : 0.004 0.031 660 Dihedral : 5.294 21.047 534 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.36), residues: 500 helix: 0.89 (0.25), residues: 384 sheet: None (None), residues: 0 loop : -1.00 (0.59), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 452 HIS 0.002 0.001 HIS B 420 PHE 0.018 0.002 PHE B 200 TYR 0.020 0.001 TYR B 103 ARG 0.002 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 GLU cc_start: 0.8218 (pm20) cc_final: 0.7619 (pm20) REVERT: B 194 THR cc_start: 0.7652 (p) cc_final: 0.7407 (p) REVERT: B 205 LEU cc_start: 0.8462 (mt) cc_final: 0.8180 (mt) REVERT: B 254 TYR cc_start: 0.8209 (m-80) cc_final: 0.7664 (m-80) REVERT: B 259 TYR cc_start: 0.7373 (m-10) cc_final: 0.6929 (m-10) REVERT: B 297 PHE cc_start: 0.8084 (m-80) cc_final: 0.7477 (m-80) REVERT: B 335 CYS cc_start: 0.9058 (m) cc_final: 0.8702 (m) REVERT: B 365 MET cc_start: 0.7757 (mmt) cc_final: 0.7119 (mmp) REVERT: B 394 PHE cc_start: 0.7689 (t80) cc_final: 0.7077 (t80) REVERT: B 398 ASN cc_start: 0.7915 (m-40) cc_final: 0.7210 (m-40) REVERT: B 415 MET cc_start: 0.9152 (tmm) cc_final: 0.8685 (ttp) REVERT: B 500 MET cc_start: 0.6501 (mmt) cc_final: 0.5510 (mtm) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.1318 time to fit residues: 24.2122 Evaluate side-chains 104 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 29 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 8 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 42 optimal weight: 0.1980 chunk 22 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 497 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.123643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.100131 restraints weight = 6361.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.103524 restraints weight = 3551.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.105754 restraints weight = 2422.773| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4033 Z= 0.172 Angle : 0.605 6.663 5505 Z= 0.300 Chirality : 0.041 0.156 665 Planarity : 0.004 0.035 660 Dihedral : 4.606 18.633 534 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.37), residues: 500 helix: 1.54 (0.25), residues: 386 sheet: None (None), residues: 0 loop : -0.74 (0.59), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 405 HIS 0.003 0.001 HIS B 319 PHE 0.014 0.001 PHE B 200 TYR 0.014 0.001 TYR B 289 ARG 0.001 0.000 ARG A 211 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.449 Fit side-chains revert: symmetry clash REVERT: A 167 GLU cc_start: 0.8411 (pm20) cc_final: 0.7712 (pm20) REVERT: B 54 ASN cc_start: 0.7355 (m-40) cc_final: 0.6904 (m-40) REVERT: B 178 CYS cc_start: 0.8551 (t) cc_final: 0.8340 (t) REVERT: B 194 THR cc_start: 0.7756 (p) cc_final: 0.7238 (p) REVERT: B 205 LEU cc_start: 0.8272 (mt) cc_final: 0.7998 (mt) REVERT: B 254 TYR cc_start: 0.8154 (m-80) cc_final: 0.7564 (m-80) REVERT: B 394 PHE cc_start: 0.7639 (t80) cc_final: 0.7327 (t80) REVERT: B 398 ASN cc_start: 0.7956 (m-40) cc_final: 0.7477 (m-40) REVERT: B 500 MET cc_start: 0.6586 (mmt) cc_final: 0.5362 (mtm) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.1304 time to fit residues: 20.7742 Evaluate side-chains 93 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 8 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 19 optimal weight: 8.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.121556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.097869 restraints weight = 6503.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.101204 restraints weight = 3685.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.103424 restraints weight = 2563.788| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.4504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4033 Z= 0.226 Angle : 0.630 7.041 5505 Z= 0.312 Chirality : 0.042 0.150 665 Planarity : 0.004 0.038 660 Dihedral : 4.434 17.817 534 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.37), residues: 500 helix: 1.59 (0.26), residues: 384 sheet: None (None), residues: 0 loop : -0.22 (0.61), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 405 HIS 0.001 0.001 HIS B 367 PHE 0.019 0.002 PHE B 473 TYR 0.021 0.001 TYR B 289 ARG 0.002 0.000 ARG A 211 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 GLU cc_start: 0.8372 (pm20) cc_final: 0.8064 (pm20) REVERT: B 46 LEU cc_start: 0.8028 (mt) cc_final: 0.7459 (mt) REVERT: B 178 CYS cc_start: 0.8534 (t) cc_final: 0.8328 (t) REVERT: B 194 THR cc_start: 0.7866 (p) cc_final: 0.7606 (p) REVERT: B 254 TYR cc_start: 0.8327 (m-80) cc_final: 0.7750 (m-80) REVERT: B 319 HIS cc_start: 0.7975 (m90) cc_final: 0.7096 (m-70) REVERT: B 365 MET cc_start: 0.8239 (mmp) cc_final: 0.7860 (mmp) REVERT: B 383 MET cc_start: 0.9182 (mmm) cc_final: 0.8949 (tpt) REVERT: B 432 ASN cc_start: 0.7158 (t0) cc_final: 0.6834 (t0) REVERT: B 500 MET cc_start: 0.6921 (mmt) cc_final: 0.5788 (mtm) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.1353 time to fit residues: 19.6490 Evaluate side-chains 87 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 30 optimal weight: 0.0470 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 42 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.9882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 398 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.124458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.101585 restraints weight = 6514.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.104907 restraints weight = 3610.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.106945 restraints weight = 2484.956| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.4856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4033 Z= 0.166 Angle : 0.581 6.349 5505 Z= 0.283 Chirality : 0.040 0.150 665 Planarity : 0.004 0.037 660 Dihedral : 4.195 17.438 534 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.38), residues: 500 helix: 1.82 (0.26), residues: 386 sheet: None (None), residues: 0 loop : -0.29 (0.62), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 405 HIS 0.002 0.001 HIS B 420 PHE 0.013 0.001 PHE B 95 TYR 0.022 0.001 TYR B 103 ARG 0.002 0.000 ARG B 419 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: A 167 GLU cc_start: 0.8436 (pm20) cc_final: 0.8132 (pm20) REVERT: B 178 CYS cc_start: 0.8551 (t) cc_final: 0.8285 (t) REVERT: B 194 THR cc_start: 0.7822 (p) cc_final: 0.7514 (p) REVERT: B 254 TYR cc_start: 0.8272 (m-80) cc_final: 0.7779 (m-80) REVERT: B 319 HIS cc_start: 0.7815 (m90) cc_final: 0.7150 (m-70) REVERT: B 394 PHE cc_start: 0.7341 (t80) cc_final: 0.7140 (t80) REVERT: B 407 CYS cc_start: 0.7131 (t) cc_final: 0.6559 (t) REVERT: B 421 ARG cc_start: 0.7526 (mmp-170) cc_final: 0.7304 (mmp80) REVERT: B 432 ASN cc_start: 0.6986 (t0) cc_final: 0.6738 (t0) REVERT: B 500 MET cc_start: 0.6936 (mmt) cc_final: 0.5815 (mtm) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1291 time to fit residues: 19.3673 Evaluate side-chains 87 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 35 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.125109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.102369 restraints weight = 6337.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.105535 restraints weight = 3559.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.107531 restraints weight = 2466.389| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.5067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4033 Z= 0.164 Angle : 0.572 6.495 5505 Z= 0.280 Chirality : 0.039 0.153 665 Planarity : 0.004 0.034 660 Dihedral : 4.078 16.362 534 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.38), residues: 500 helix: 1.97 (0.26), residues: 387 sheet: None (None), residues: 0 loop : -0.28 (0.60), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 257 HIS 0.001 0.000 HIS B 367 PHE 0.013 0.001 PHE B 95 TYR 0.023 0.001 TYR B 103 ARG 0.001 0.000 ARG A 211 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.451 Fit side-chains revert: symmetry clash REVERT: A 167 GLU cc_start: 0.8424 (pm20) cc_final: 0.8121 (pm20) REVERT: B 105 GLU cc_start: 0.5660 (tp30) cc_final: 0.5273 (tp30) REVERT: B 136 GLU cc_start: 0.7283 (mm-30) cc_final: 0.6674 (mm-30) REVERT: B 178 CYS cc_start: 0.8556 (t) cc_final: 0.8320 (t) REVERT: B 254 TYR cc_start: 0.7979 (m-80) cc_final: 0.7441 (m-80) REVERT: B 383 MET cc_start: 0.9161 (mmm) cc_final: 0.8952 (tpt) REVERT: B 421 ARG cc_start: 0.7507 (mmp-170) cc_final: 0.7214 (mmp-170) REVERT: B 500 MET cc_start: 0.6962 (mmt) cc_final: 0.5875 (mtm) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.1315 time to fit residues: 18.6030 Evaluate side-chains 89 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 12 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 chunk 7 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.126156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.102772 restraints weight = 6324.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.105948 restraints weight = 3563.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.108309 restraints weight = 2476.111| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.5164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4033 Z= 0.163 Angle : 0.592 7.710 5505 Z= 0.284 Chirality : 0.040 0.154 665 Planarity : 0.004 0.035 660 Dihedral : 4.083 18.870 534 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.38), residues: 500 helix: 2.06 (0.26), residues: 387 sheet: None (None), residues: 0 loop : -0.26 (0.60), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 257 HIS 0.001 0.000 HIS B 367 PHE 0.019 0.001 PHE B 474 TYR 0.019 0.001 TYR B 103 ARG 0.001 0.000 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.452 Fit side-chains revert: symmetry clash REVERT: A 167 GLU cc_start: 0.8439 (pm20) cc_final: 0.7874 (pm20) REVERT: B 136 GLU cc_start: 0.7329 (mm-30) cc_final: 0.6869 (mm-30) REVERT: B 178 CYS cc_start: 0.8542 (t) cc_final: 0.8268 (t) REVERT: B 194 THR cc_start: 0.7613 (p) cc_final: 0.7401 (p) REVERT: B 254 TYR cc_start: 0.7945 (m-80) cc_final: 0.7460 (m-80) REVERT: B 305 MET cc_start: 0.8803 (mmm) cc_final: 0.8533 (mmm) REVERT: B 421 ARG cc_start: 0.7545 (mmp-170) cc_final: 0.7221 (mmp-170) REVERT: B 500 MET cc_start: 0.6992 (mmt) cc_final: 0.5888 (mtm) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.1316 time to fit residues: 18.9942 Evaluate side-chains 89 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 41 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.125610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.102487 restraints weight = 6376.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.105679 restraints weight = 3640.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.107888 restraints weight = 2549.792| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.5219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4033 Z= 0.185 Angle : 0.607 7.156 5505 Z= 0.296 Chirality : 0.041 0.149 665 Planarity : 0.004 0.034 660 Dihedral : 4.073 16.247 534 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.38), residues: 500 helix: 1.96 (0.26), residues: 390 sheet: None (None), residues: 0 loop : -0.20 (0.62), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 257 HIS 0.005 0.001 HIS B 319 PHE 0.019 0.001 PHE B 474 TYR 0.020 0.001 TYR B 103 ARG 0.001 0.000 ARG A 211 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 GLU cc_start: 0.8521 (pm20) cc_final: 0.7954 (pm20) REVERT: A 209 ARG cc_start: 0.6426 (mmt180) cc_final: 0.6066 (mmm-85) REVERT: B 178 CYS cc_start: 0.8674 (t) cc_final: 0.8429 (t) REVERT: B 194 THR cc_start: 0.7606 (p) cc_final: 0.7370 (p) REVERT: B 254 TYR cc_start: 0.8175 (m-80) cc_final: 0.7597 (m-80) REVERT: B 291 LEU cc_start: 0.8375 (mm) cc_final: 0.8150 (mm) REVERT: B 300 LEU cc_start: 0.9153 (mt) cc_final: 0.8933 (mt) REVERT: B 305 MET cc_start: 0.8926 (mmm) cc_final: 0.8586 (mmt) REVERT: B 500 MET cc_start: 0.6977 (mmt) cc_final: 0.5930 (mtm) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1285 time to fit residues: 18.5609 Evaluate side-chains 93 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 28 optimal weight: 0.9980 chunk 13 optimal weight: 7.9990 chunk 41 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.125969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.102497 restraints weight = 6398.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.105825 restraints weight = 3619.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.108023 restraints weight = 2513.902| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.5348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4033 Z= 0.183 Angle : 0.640 8.505 5505 Z= 0.308 Chirality : 0.042 0.221 665 Planarity : 0.004 0.034 660 Dihedral : 4.047 16.342 534 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.38), residues: 500 helix: 1.94 (0.26), residues: 390 sheet: None (None), residues: 0 loop : -0.14 (0.62), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 405 HIS 0.007 0.002 HIS B 319 PHE 0.023 0.002 PHE B 439 TYR 0.028 0.001 TYR B 103 ARG 0.001 0.000 ARG B 348 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 GLU cc_start: 0.8516 (pm20) cc_final: 0.7964 (pm20) REVERT: A 209 ARG cc_start: 0.6416 (mmt180) cc_final: 0.5991 (mmm-85) REVERT: B 178 CYS cc_start: 0.8621 (t) cc_final: 0.8337 (t) REVERT: B 254 TYR cc_start: 0.8062 (m-80) cc_final: 0.7460 (m-80) REVERT: B 291 LEU cc_start: 0.8348 (mm) cc_final: 0.8073 (mm) REVERT: B 300 LEU cc_start: 0.9132 (mt) cc_final: 0.8923 (mt) REVERT: B 305 MET cc_start: 0.8964 (mmm) cc_final: 0.8618 (mmt) REVERT: B 421 ARG cc_start: 0.7876 (mmp-170) cc_final: 0.7355 (mmp80) REVERT: B 500 MET cc_start: 0.6940 (mmt) cc_final: 0.5896 (mtm) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.1286 time to fit residues: 17.8862 Evaluate side-chains 92 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 49 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 13 optimal weight: 7.9990 chunk 9 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 398 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.126710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.103693 restraints weight = 6258.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.107092 restraints weight = 3503.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.109095 restraints weight = 2400.985| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.5497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4033 Z= 0.165 Angle : 0.619 7.087 5505 Z= 0.298 Chirality : 0.041 0.144 665 Planarity : 0.004 0.034 660 Dihedral : 3.971 16.829 534 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.38), residues: 500 helix: 2.01 (0.26), residues: 390 sheet: None (None), residues: 0 loop : -0.10 (0.62), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 405 HIS 0.005 0.001 HIS B 319 PHE 0.028 0.002 PHE B 439 TYR 0.025 0.001 TYR B 103 ARG 0.001 0.000 ARG A 182 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 167 GLU cc_start: 0.8485 (pm20) cc_final: 0.7964 (pm20) REVERT: A 209 ARG cc_start: 0.6378 (mmt180) cc_final: 0.5944 (mmm-85) REVERT: B 178 CYS cc_start: 0.8595 (t) cc_final: 0.8310 (t) REVERT: B 254 TYR cc_start: 0.8032 (m-80) cc_final: 0.7447 (m-80) REVERT: B 265 GLU cc_start: 0.7011 (mt-10) cc_final: 0.6807 (mp0) REVERT: B 291 LEU cc_start: 0.8317 (mm) cc_final: 0.8070 (mm) REVERT: B 300 LEU cc_start: 0.9097 (mt) cc_final: 0.8791 (mt) REVERT: B 305 MET cc_start: 0.8951 (mmm) cc_final: 0.8586 (mmt) REVERT: B 421 ARG cc_start: 0.7873 (mmp-170) cc_final: 0.7359 (mmp80) REVERT: B 500 MET cc_start: 0.6993 (mmt) cc_final: 0.6134 (mtm) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.1201 time to fit residues: 16.7028 Evaluate side-chains 87 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 47 optimal weight: 9.9990 chunk 27 optimal weight: 0.1980 chunk 48 optimal weight: 9.9990 chunk 9 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.128031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.105256 restraints weight = 6107.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.108342 restraints weight = 3450.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.110666 restraints weight = 2390.854| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.5573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4033 Z= 0.166 Angle : 0.624 7.203 5505 Z= 0.300 Chirality : 0.041 0.146 665 Planarity : 0.004 0.033 660 Dihedral : 3.981 16.879 534 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.38), residues: 500 helix: 1.99 (0.26), residues: 391 sheet: None (None), residues: 0 loop : -0.02 (0.62), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 405 HIS 0.008 0.002 HIS B 367 PHE 0.025 0.001 PHE B 439 TYR 0.011 0.001 TYR B 289 ARG 0.001 0.000 ARG A 211 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1383.15 seconds wall clock time: 24 minutes 59.43 seconds (1499.43 seconds total)