Starting phenix.real_space_refine on Thu Mar 6 03:40:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/1oed_1044/03_2025/1oed_1044.cif Found real_map, /net/cci-nas-00/data/ceres_data/1oed_1044/03_2025/1oed_1044.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/1oed_1044/03_2025/1oed_1044.map" default_real_map = "/net/cci-nas-00/data/ceres_data/1oed_1044/03_2025/1oed_1044.map" model { file = "/net/cci-nas-00/data/ceres_data/1oed_1044/03_2025/1oed_1044.cif" } default_model = "/net/cci-nas-00/data/ceres_data/1oed_1044/03_2025/1oed_1044.cif" } resolution = 4.0 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 ------------------------------------------------------------------------------- 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= -0.000 sd= 1.000 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 37 5.16 5 C 3331 2.51 5 N 735 2.21 5 O 823 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 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: 4926 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 978 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "B" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 995 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 7, 'TRANS': 119} Chain breaks: 1 Chain: "C" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 982 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 7, 'TRANS': 119} Chain breaks: 1 Chain: "D" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 978 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "E" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 993 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain breaks: 1 Time building chain proxies: 3.36, per 1000 atoms: 0.68 Number of scatterers: 4926 At special positions: 0 Unit cell: (96, 88, 67, 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 37 16.00 O 823 8.00 N 735 7.00 C 3331 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.52 Conformation dependent library (CDL) restraints added in 544.6 milliseconds 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1218 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 92.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 212 through 239 removed outlier: 3.584A pdb=" N VAL A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASN A 217 " --> pdb=" O TYR A 213 " (cutoff:3.500A) Proline residue: A 221 - end of helix Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 242 through 271 removed outlier: 3.660A pdb=" N GLU A 262 " --> pdb=" O LEU A 258 " (cutoff:3.500A) Proline residue: A 265 - end of helix Processing helix chain 'A' and resid 275 through 302 removed outlier: 3.935A pdb=" N PHE A 280 " --> pdb=" O LYS A 276 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N THR A 281 " --> pdb=" O TYR A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 437 Processing helix chain 'B' and resid 218 through 245 removed outlier: 3.668A pdb=" N VAL B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR B 223 " --> pdb=" O PHE B 219 " (cutoff:3.500A) Proline residue: B 227 - end of helix Proline residue: B 242 - end of helix Processing helix chain 'B' and resid 248 through 277 removed outlier: 3.500A pdb=" N ALA B 255 " --> pdb=" O LEU B 251 " (cutoff:3.500A) Proline residue: B 271 - end of helix removed outlier: 3.781A pdb=" N LEU B 275 " --> pdb=" O PRO B 271 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER B 276 " --> pdb=" O GLU B 272 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL B 277 " --> pdb=" O THR B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 307 removed outlier: 4.130A pdb=" N ILE B 289 " --> pdb=" O MET B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 462 Processing helix chain 'C' and resid 226 through 253 removed outlier: 4.092A pdb=" N ASN C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) Proline residue: C 235 - end of helix Proline residue: C 250 - end of helix Processing helix chain 'C' and resid 256 through 285 Proline residue: C 279 - end of helix Processing helix chain 'C' and resid 289 through 316 removed outlier: 3.916A pdb=" N PHE C 294 " --> pdb=" O LYS C 290 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE C 295 " --> pdb=" O TYR C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 484 Proline residue: C 463 - end of helix Proline residue: C 481 - end of helix Processing helix chain 'D' and resid 212 through 239 removed outlier: 3.582A pdb=" N VAL D 216 " --> pdb=" O LEU D 212 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASN D 217 " --> pdb=" O TYR D 213 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE D 219 " --> pdb=" O VAL D 215 " (cutoff:3.500A) Proline residue: D 221 - end of helix Proline residue: D 236 - end of helix Processing helix chain 'D' and resid 242 through 271 removed outlier: 3.660A pdb=" N GLU D 262 " --> pdb=" O LEU D 258 " (cutoff:3.500A) Proline residue: D 265 - end of helix Processing helix chain 'D' and resid 275 through 302 removed outlier: 3.936A pdb=" N PHE D 280 " --> pdb=" O LYS D 276 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR D 281 " --> pdb=" O TYR D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 437 Processing helix chain 'E' and resid 221 through 246 Proline residue: E 229 - end of helix removed outlier: 3.979A pdb=" N SER E 234 " --> pdb=" O CYS E 230 " (cutoff:3.500A) Proline residue: E 244 - end of helix Processing helix chain 'E' and resid 250 through 280 Proline residue: E 274 - end of helix Processing helix chain 'E' and resid 285 through 311 Processing helix chain 'E' and resid 445 through 478 Proline residue: E 476 - end of helix 435 hydrogen bonds defined for protein. 1305 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: 1.22 Time building geometry restraints manager: 1.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 751 1.31 - 1.43: 1242 1.43 - 1.56: 2970 1.56 - 1.69: 6 1.69 - 1.82: 61 Bond restraints: 5030 Sorted by residual: bond pdb=" N PRO B 271 " pdb=" CD PRO B 271 " ideal model delta sigma weight residual 1.473 1.221 0.252 1.40e-02 5.10e+03 3.23e+02 bond pdb=" C ALA A 403 " pdb=" O ALA A 403 " ideal model delta sigma weight residual 1.231 1.384 -0.153 2.00e-02 2.50e+03 5.87e+01 bond pdb=" C ALA D 403 " pdb=" O ALA D 403 " ideal model delta sigma weight residual 1.231 1.384 -0.153 2.00e-02 2.50e+03 5.86e+01 bond pdb=" CB VAL B 445 " pdb=" CG1 VAL B 445 " ideal model delta sigma weight residual 1.521 1.721 -0.200 3.30e-02 9.18e+02 3.69e+01 bond pdb=" N PRO B 464 " pdb=" CD PRO B 464 " ideal model delta sigma weight residual 1.473 1.549 -0.076 1.40e-02 5.10e+03 2.92e+01 ... (remaining 5025 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 5620 2.74 - 5.47: 1040 5.47 - 8.21: 136 8.21 - 10.95: 50 10.95 - 13.68: 9 Bond angle restraints: 6855 Sorted by residual: angle pdb=" OE1 GLN E 474 " pdb=" CD GLN E 474 " pdb=" NE2 GLN E 474 " ideal model delta sigma weight residual 122.60 112.76 9.84 1.00e+00 1.00e+00 9.69e+01 angle pdb=" OE1 GLN A 435 " pdb=" CD GLN A 435 " pdb=" NE2 GLN A 435 " ideal model delta sigma weight residual 122.60 112.77 9.83 1.00e+00 1.00e+00 9.67e+01 angle pdb=" OE1 GLN E 262 " pdb=" CD GLN E 262 " pdb=" NE2 GLN E 262 " ideal model delta sigma weight residual 122.60 112.81 9.79 1.00e+00 1.00e+00 9.59e+01 angle pdb=" OE1 GLN E 246 " pdb=" CD GLN E 246 " pdb=" NE2 GLN E 246 " ideal model delta sigma weight residual 122.60 112.84 9.76 1.00e+00 1.00e+00 9.52e+01 angle pdb=" CA THR C 462 " pdb=" C THR C 462 " pdb=" N PRO C 463 " ideal model delta sigma weight residual 120.77 111.31 9.46 9.70e-01 1.06e+00 9.51e+01 ... (remaining 6850 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 2582 17.92 - 35.83: 266 35.83 - 53.75: 111 53.75 - 71.67: 12 71.67 - 89.59: 4 Dihedral angle restraints: 2975 sinusoidal: 1114 harmonic: 1861 Sorted by residual: dihedral pdb=" C PRO E 476 " pdb=" N PRO E 476 " pdb=" CA PRO E 476 " pdb=" CB PRO E 476 " ideal model delta harmonic sigma weight residual -120.70 -109.72 -10.98 0 2.50e+00 1.60e-01 1.93e+01 dihedral pdb=" C PRO D 236 " pdb=" N PRO D 236 " pdb=" CA PRO D 236 " pdb=" CB PRO D 236 " ideal model delta harmonic sigma weight residual -120.70 -109.89 -10.81 0 2.50e+00 1.60e-01 1.87e+01 dihedral pdb=" C PRO A 236 " pdb=" N PRO A 236 " pdb=" CA PRO A 236 " pdb=" CB PRO A 236 " ideal model delta harmonic sigma weight residual -120.70 -109.91 -10.79 0 2.50e+00 1.60e-01 1.86e+01 ... (remaining 2972 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.276: 898 0.276 - 0.552: 5 0.552 - 0.827: 0 0.827 - 1.103: 0 1.103 - 1.379: 1 Chirality restraints: 904 Sorted by residual: chirality pdb=" CB VAL B 445 " pdb=" CA VAL B 445 " pdb=" CG1 VAL B 445 " pdb=" CG2 VAL B 445 " both_signs ideal model delta sigma weight residual False -2.63 -4.01 1.38 2.00e-01 2.50e+01 4.75e+01 chirality pdb=" CB ILE B 446 " pdb=" CA ILE B 446 " pdb=" CG1 ILE B 446 " pdb=" CG2 ILE B 446 " both_signs ideal model delta sigma weight residual False 2.64 3.17 -0.52 2.00e-01 2.50e+01 6.82e+00 chirality pdb=" CA HIS E 471 " pdb=" N HIS E 471 " pdb=" C HIS E 471 " pdb=" CB HIS E 471 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.48e+00 ... (remaining 901 not shown) Planarity restraints: 798 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO E 476 " -0.039 2.00e-02 2.50e+03 8.13e-02 6.62e+01 pdb=" C PRO E 476 " 0.141 2.00e-02 2.50e+03 pdb=" O PRO E 476 " -0.054 2.00e-02 2.50e+03 pdb=" N GLU E 477 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 275 " 0.026 2.00e-02 2.50e+03 4.99e-02 2.49e+01 pdb=" C LEU B 275 " -0.086 2.00e-02 2.50e+03 pdb=" O LEU B 275 " 0.031 2.00e-02 2.50e+03 pdb=" N SER B 276 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS E 445 " 0.019 2.00e-02 2.50e+03 4.20e-02 1.76e+01 pdb=" C LYS E 445 " -0.072 2.00e-02 2.50e+03 pdb=" O LYS E 445 " 0.029 2.00e-02 2.50e+03 pdb=" N VAL E 446 " 0.024 2.00e-02 2.50e+03 ... (remaining 795 not shown) Histogram of nonbonded interaction distances: 1.18 - 1.93: 21 1.93 - 2.67: 595 2.67 - 3.41: 8998 3.41 - 4.16: 13035 4.16 - 4.90: 21585 Nonbonded interactions: 44234 Sorted by model distance: nonbonded pdb=" O TYR E 241 " pdb=" CG PRO E 244 " model vdw 1.183 3.440 nonbonded pdb=" O HIS B 460 " pdb=" CD PRO B 464 " model vdw 1.352 3.440 nonbonded pdb=" O TYR E 241 " pdb=" CD PRO E 244 " model vdw 1.447 3.440 nonbonded pdb=" O PHE B 239 " pdb=" CD PRO B 242 " model vdw 1.624 3.440 nonbonded pdb=" O PHE C 459 " pdb=" CD PRO C 463 " model vdw 1.640 3.440 ... (remaining 44229 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } 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: 0.070 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.350 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1921 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 : 0.014 0.252 5030 Z= 0.934 Angle : 2.288 13.685 6855 Z= 1.670 Chirality : 0.097 1.379 904 Planarity : 0.009 0.081 798 Dihedral : 17.230 89.585 1757 Min Nonbonded Distance : 1.183 Molprobity Statistics. All-atom Clashscore : 224.94 Ramachandran Plot: Outliers : 2.11 % Allowed : 5.19 % Favored : 92.69 % Rotamer: Outliers : 19.76 % Allowed : 14.04 % Favored : 66.20 % Cbeta Deviations : 0.49 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.67 (0.27), residues: 616 helix: -2.15 (0.18), residues: 512 sheet: None (None), residues: 0 loop : -2.61 (0.54), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.005 TRP E 453 HIS 0.006 0.001 HIS B 460 PHE 0.021 0.002 PHE C 247 TYR 0.014 0.001 TYR B 220 ARG 0.001 0.000 ARG E 310 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 111 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 PHE cc_start: 0.4349 (OUTLIER) cc_final: 0.4004 (m-80) REVERT: A 284 PHE cc_start: 0.2953 (OUTLIER) cc_final: 0.2420 (t80) REVERT: A 411 LEU cc_start: 0.5778 (OUTLIER) cc_final: 0.4758 (mm) REVERT: C 457 SER cc_start: -0.6578 (OUTLIER) cc_final: -0.7210 (m) REVERT: C 462 THR cc_start: 0.6349 (m) cc_final: 0.5915 (m) REVERT: C 475 MET cc_start: 0.0883 (OUTLIER) cc_final: -0.0572 (mtt) REVERT: C 479 ASN cc_start: -0.2803 (OUTLIER) cc_final: -0.3292 (t0) REVERT: D 243 MET cc_start: 0.3821 (mtt) cc_final: 0.2367 (pmm) REVERT: D 298 THR cc_start: 0.5185 (OUTLIER) cc_final: 0.4842 (m) REVERT: D 302 SER cc_start: 0.6645 (OUTLIER) cc_final: 0.5667 (t) REVERT: E 272 LYS cc_start: 0.5415 (OUTLIER) cc_final: 0.4499 (tttt) REVERT: E 297 ILE cc_start: 0.1827 (OUTLIER) cc_final: 0.1572 (tp) outliers start: 114 outliers final: 46 residues processed: 198 average time/residue: 0.1421 time to fit residues: 36.6181 Evaluate side-chains 128 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 72 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 280 PHE Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 426 PHE Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 282 ARG Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 437 ARG Chi-restraints excluded: chain B residue 441 TYR Chi-restraints excluded: chain B residue 444 PHE Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 241 PHE Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 314 PHE Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 457 SER Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 422 THR Chi-restraints excluded: chain D residue 432 GLU Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 272 LYS Chi-restraints excluded: chain E residue 286 TYR Chi-restraints excluded: chain E residue 297 ILE Chi-restraints excluded: chain E residue 308 SER Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 453 TRP Chi-restraints excluded: chain E residue 463 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 30.0000 chunk 45 optimal weight: 20.0000 chunk 25 optimal weight: 50.0000 chunk 15 optimal weight: 30.0000 chunk 30 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 47 optimal weight: 50.0000 chunk 18 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 35 optimal weight: 9.9990 chunk 54 optimal weight: 0.0980 overall best weight: 7.2190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 GLN ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 305 ASN C 479 ASN D 217 ASN ** D 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.122109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.105149 restraints weight = 43851.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.104024 restraints weight = 55847.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.104012 restraints weight = 61945.917| |-----------------------------------------------------------------------------| r_work (final): 0.4366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3387 moved from start: 0.5985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 5030 Z= 0.436 Angle : 1.144 11.708 6855 Z= 0.582 Chirality : 0.055 0.316 904 Planarity : 0.009 0.068 798 Dihedral : 13.847 84.525 764 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 39.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 10.05 % Allowed : 17.33 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.65 (0.32), residues: 616 helix: -0.77 (0.21), residues: 567 sheet: None (None), residues: 0 loop : -2.70 (0.83), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP E 453 HIS 0.007 0.002 HIS D 300 PHE 0.036 0.004 PHE B 286 TYR 0.033 0.003 TYR C 248 ARG 0.004 0.001 ARG D 301 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 73 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 PHE cc_start: 0.7382 (t80) cc_final: 0.7044 (m-10) REVERT: B 293 PHE cc_start: 0.8131 (OUTLIER) cc_final: 0.7857 (t80) REVERT: B 433 MET cc_start: 0.3744 (mpp) cc_final: 0.1860 (mpp) REVERT: B 440 LEU cc_start: 0.6860 (OUTLIER) cc_final: 0.6623 (tp) REVERT: C 257 MET cc_start: -0.3863 (mtt) cc_final: -0.4070 (mtt) REVERT: C 296 MET cc_start: 0.6332 (mmp) cc_final: 0.5639 (mtp) REVERT: D 243 MET cc_start: 0.4818 (mtt) cc_final: 0.3700 (pmm) outliers start: 58 outliers final: 21 residues processed: 115 average time/residue: 0.1362 time to fit residues: 20.9394 Evaluate side-chains 84 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 61 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 282 ARG Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 422 THR Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 286 TYR Chi-restraints excluded: chain E residue 453 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 26 optimal weight: 40.0000 chunk 3 optimal weight: 7.9990 chunk 53 optimal weight: 8.9990 chunk 51 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 29 optimal weight: 0.2980 chunk 38 optimal weight: 10.0000 chunk 4 optimal weight: 8.9990 chunk 5 optimal weight: 50.0000 chunk 44 optimal weight: 7.9990 overall best weight: 6.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 ASN C 267 GLN C 305 ASN C 313 HIS ** D 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.119762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.102712 restraints weight = 44948.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.102678 restraints weight = 50879.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.102078 restraints weight = 51946.946| |-----------------------------------------------------------------------------| r_work (final): 0.4372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3554 moved from start: 0.8184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 5030 Z= 0.337 Angle : 0.972 11.336 6855 Z= 0.480 Chirality : 0.048 0.278 904 Planarity : 0.007 0.069 798 Dihedral : 9.803 79.757 687 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 27.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 5.55 % Allowed : 18.89 % Favored : 75.56 % 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: -0.91 (0.32), residues: 616 helix: -0.30 (0.21), residues: 549 sheet: None (None), residues: 0 loop : -1.82 (0.69), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 453 HIS 0.006 0.001 HIS B 306 PHE 0.023 0.003 PHE C 314 TYR 0.008 0.001 TYR A 234 ARG 0.009 0.001 ARG B 437 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 70 time to evaluate : 0.595 Fit side-chains revert: symmetry clash REVERT: A 426 PHE cc_start: 0.7466 (t80) cc_final: 0.6998 (m-10) REVERT: B 236 ILE cc_start: -0.0440 (OUTLIER) cc_final: -0.0712 (tp) REVERT: B 289 ILE cc_start: 0.7712 (OUTLIER) cc_final: 0.7452 (mm) REVERT: C 296 MET cc_start: 0.6565 (mmp) cc_final: 0.6203 (ptm) REVERT: C 475 MET cc_start: -0.2450 (ptt) cc_final: -0.3818 (mmt) REVERT: D 243 MET cc_start: 0.4989 (mtt) cc_final: 0.4109 (pmm) REVERT: D 435 GLN cc_start: -0.2625 (OUTLIER) cc_final: -0.2997 (mt0) outliers start: 32 outliers final: 15 residues processed: 96 average time/residue: 0.1269 time to fit residues: 16.6842 Evaluate side-chains 76 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 422 THR Chi-restraints excluded: chain D residue 435 GLN Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 286 TYR Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 453 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 40.0000 chunk 45 optimal weight: 30.0000 chunk 52 optimal weight: 10.0000 chunk 57 optimal weight: 8.9990 chunk 21 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 54 optimal weight: 0.8980 chunk 51 optimal weight: 10.0000 overall best weight: 7.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 ASN D 300 HIS E 225 ASN ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.117753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.101106 restraints weight = 45319.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.099489 restraints weight = 57231.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.098755 restraints weight = 74590.650| |-----------------------------------------------------------------------------| r_work (final): 0.4325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3766 moved from start: 0.9735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 5030 Z= 0.309 Angle : 0.909 11.185 6855 Z= 0.445 Chirality : 0.046 0.214 904 Planarity : 0.007 0.068 798 Dihedral : 8.405 72.343 676 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 25.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.85 % Allowed : 20.97 % Favored : 74.18 % 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: -0.10 (0.32), residues: 616 helix: 0.21 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -1.45 (0.78), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 453 HIS 0.004 0.001 HIS D 299 PHE 0.020 0.002 PHE C 314 TYR 0.012 0.002 TYR C 248 ARG 0.003 0.001 ARG C 277 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 69 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 PHE cc_start: 0.7700 (t80) cc_final: 0.7123 (m-10) REVERT: B 249 MET cc_start: 0.2736 (mmp) cc_final: 0.1934 (pmm) REVERT: C 296 MET cc_start: 0.6649 (mmp) cc_final: 0.6242 (ptm) REVERT: C 475 MET cc_start: -0.2477 (ptt) cc_final: -0.3711 (mmt) REVERT: D 243 MET cc_start: 0.5286 (mtt) cc_final: 0.4465 (pmm) REVERT: D 435 GLN cc_start: -0.1808 (OUTLIER) cc_final: -0.2204 (mt0) REVERT: E 453 TRP cc_start: 0.6508 (OUTLIER) cc_final: 0.6231 (m100) outliers start: 28 outliers final: 17 residues processed: 91 average time/residue: 0.1086 time to fit residues: 14.2052 Evaluate side-chains 80 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 441 TYR Chi-restraints excluded: chain C residue 236 CYS Chi-restraints excluded: chain C residue 241 PHE Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 422 THR Chi-restraints excluded: chain D residue 435 GLN Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 286 TYR Chi-restraints excluded: chain E residue 453 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 45 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 47 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 479 ASN E 225 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.116103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.099865 restraints weight = 44926.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.097976 restraints weight = 61308.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.097844 restraints weight = 71964.368| |-----------------------------------------------------------------------------| r_work (final): 0.4301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3935 moved from start: 1.1016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 5030 Z= 0.307 Angle : 0.897 12.280 6855 Z= 0.432 Chirality : 0.045 0.195 904 Planarity : 0.008 0.068 798 Dihedral : 7.445 58.156 670 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 21.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.81 % Allowed : 21.66 % Favored : 74.52 % 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: 0.74 (0.33), residues: 616 helix: 0.76 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -1.19 (0.81), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP E 453 HIS 0.005 0.001 HIS B 460 PHE 0.023 0.002 PHE D 256 TYR 0.014 0.001 TYR B 220 ARG 0.008 0.001 ARG B 282 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 0.512 Fit side-chains revert: symmetry clash REVERT: A 426 PHE cc_start: 0.7626 (t80) cc_final: 0.7071 (m-10) REVERT: B 249 MET cc_start: 0.3318 (mmt) cc_final: 0.3042 (pmm) REVERT: B 285 MET cc_start: 0.6898 (tpt) cc_final: 0.6533 (tpt) REVERT: C 296 MET cc_start: 0.6635 (mmp) cc_final: 0.6302 (ptm) REVERT: D 243 MET cc_start: 0.4980 (mtt) cc_final: 0.4707 (pmm) REVERT: E 221 PHE cc_start: 0.6317 (OUTLIER) cc_final: 0.5710 (m-80) REVERT: E 286 TYR cc_start: 0.1044 (OUTLIER) cc_final: 0.0744 (m-10) outliers start: 22 outliers final: 13 residues processed: 80 average time/residue: 0.1281 time to fit residues: 14.4486 Evaluate side-chains 67 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 441 TYR Chi-restraints excluded: chain C residue 236 CYS Chi-restraints excluded: chain C residue 241 PHE Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 294 PHE Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 286 TYR Chi-restraints excluded: chain E residue 309 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 27 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 6 optimal weight: 40.0000 chunk 51 optimal weight: 9.9990 chunk 30 optimal weight: 0.9980 chunk 11 optimal weight: 50.0000 chunk 50 optimal weight: 9.9990 chunk 46 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 57 optimal weight: 9.9990 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 271 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.114413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.096635 restraints weight = 44280.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.096007 restraints weight = 63808.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.095664 restraints weight = 77570.654| |-----------------------------------------------------------------------------| r_work (final): 0.4321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4016 moved from start: 1.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 5030 Z= 0.278 Angle : 0.876 11.893 6855 Z= 0.422 Chirality : 0.044 0.217 904 Planarity : 0.007 0.063 798 Dihedral : 6.097 59.269 662 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 21.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.64 % Allowed : 21.84 % Favored : 74.52 % 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: 1.22 (0.34), residues: 616 helix: 1.15 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -1.61 (0.75), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 453 HIS 0.008 0.001 HIS D 300 PHE 0.023 0.002 PHE C 314 TYR 0.011 0.001 TYR E 241 ARG 0.003 0.001 ARG B 282 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 60 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 VAL cc_start: 0.5235 (OUTLIER) cc_final: 0.5017 (p) REVERT: A 426 PHE cc_start: 0.7668 (t80) cc_final: 0.7155 (m-10) REVERT: B 249 MET cc_start: 0.3722 (mmt) cc_final: 0.3475 (pmm) REVERT: B 285 MET cc_start: 0.6853 (tpt) cc_final: 0.6412 (tpt) REVERT: B 289 ILE cc_start: 0.8240 (mm) cc_final: 0.8014 (mm) REVERT: C 296 MET cc_start: 0.6947 (mmp) cc_final: 0.6569 (ptm) REVERT: D 243 MET cc_start: 0.5229 (mtt) cc_final: 0.4978 (pmm) outliers start: 21 outliers final: 14 residues processed: 79 average time/residue: 0.1316 time to fit residues: 14.2559 Evaluate side-chains 72 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 441 TYR Chi-restraints excluded: chain C residue 236 CYS Chi-restraints excluded: chain C residue 241 PHE Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 286 TYR Chi-restraints excluded: chain E residue 309 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 7.9990 chunk 39 optimal weight: 50.0000 chunk 47 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 42 optimal weight: 0.9980 chunk 31 optimal weight: 20.0000 chunk 46 optimal weight: 20.0000 chunk 40 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 38 optimal weight: 20.0000 chunk 32 optimal weight: 6.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 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 = 0.4666 r_free = 0.4666 target = 0.113253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.095714 restraints weight = 43539.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.095641 restraints weight = 53638.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.095576 restraints weight = 58474.491| |-----------------------------------------------------------------------------| r_work (final): 0.4324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4111 moved from start: 1.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5030 Z= 0.275 Angle : 0.902 12.745 6855 Z= 0.431 Chirality : 0.044 0.172 904 Planarity : 0.007 0.060 798 Dihedral : 6.083 59.079 662 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 22.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.95 % Allowed : 22.70 % Favored : 74.35 % 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: 1.44 (0.34), residues: 616 helix: 1.32 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -1.72 (0.72), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 453 HIS 0.012 0.002 HIS B 306 PHE 0.022 0.002 PHE C 314 TYR 0.012 0.001 TYR E 241 ARG 0.005 0.001 ARG D 301 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.539 Fit side-chains revert: symmetry clash REVERT: A 426 PHE cc_start: 0.7548 (t80) cc_final: 0.7090 (m-10) REVERT: B 285 MET cc_start: 0.7090 (tpt) cc_final: 0.6627 (tpt) REVERT: B 289 ILE cc_start: 0.8248 (mm) cc_final: 0.8011 (mm) REVERT: C 296 MET cc_start: 0.6971 (mmp) cc_final: 0.6594 (ptm) REVERT: E 221 PHE cc_start: 0.6625 (OUTLIER) cc_final: 0.5701 (m-10) REVERT: E 272 LYS cc_start: 0.7456 (pttt) cc_final: 0.6931 (tttt) outliers start: 17 outliers final: 13 residues processed: 79 average time/residue: 0.1210 time to fit residues: 13.4707 Evaluate side-chains 74 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 441 TYR Chi-restraints excluded: chain C residue 236 CYS Chi-restraints excluded: chain C residue 241 PHE Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 294 PHE Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 309 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 19 optimal weight: 50.0000 chunk 38 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 chunk 32 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 29 optimal weight: 20.0000 chunk 5 optimal weight: 30.0000 chunk 8 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 10 optimal weight: 40.0000 overall best weight: 9.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 479 ASN E 271 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.110485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.092640 restraints weight = 43733.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.092521 restraints weight = 53015.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.092291 restraints weight = 67421.743| |-----------------------------------------------------------------------------| r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4499 moved from start: 1.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 5030 Z= 0.310 Angle : 0.966 11.210 6855 Z= 0.467 Chirality : 0.046 0.203 904 Planarity : 0.008 0.062 798 Dihedral : 6.262 59.181 660 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 24.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.29 % Allowed : 23.05 % Favored : 73.66 % 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: 1.19 (0.34), residues: 616 helix: 1.19 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -2.25 (0.70), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP E 453 HIS 0.009 0.002 HIS D 300 PHE 0.028 0.002 PHE D 256 TYR 0.038 0.003 TYR A 213 ARG 0.004 0.001 ARG D 301 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 426 PHE cc_start: 0.7858 (t80) cc_final: 0.7059 (m-10) REVERT: C 296 MET cc_start: 0.7336 (mmp) cc_final: 0.6913 (ptm) outliers start: 19 outliers final: 15 residues processed: 80 average time/residue: 0.1162 time to fit residues: 13.0585 Evaluate side-chains 75 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 441 TYR Chi-restraints excluded: chain C residue 236 CYS Chi-restraints excluded: chain C residue 241 PHE Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 294 PHE Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 309 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 24 optimal weight: 30.0000 chunk 1 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 34 optimal weight: 0.6980 chunk 50 optimal weight: 30.0000 chunk 25 optimal weight: 9.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 225 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 = 0.4649 r_free = 0.4649 target = 0.111165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.093086 restraints weight = 43472.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.092355 restraints weight = 56672.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.092306 restraints weight = 59919.305| |-----------------------------------------------------------------------------| r_work (final): 0.4281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4376 moved from start: 1.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5030 Z= 0.282 Angle : 0.960 13.576 6855 Z= 0.458 Chirality : 0.047 0.301 904 Planarity : 0.007 0.058 798 Dihedral : 6.049 58.833 660 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 22.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.95 % Allowed : 24.61 % Favored : 72.44 % 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: 1.49 (0.34), residues: 616 helix: 1.39 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -1.99 (0.74), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 453 HIS 0.008 0.001 HIS D 300 PHE 0.026 0.002 PHE D 256 TYR 0.018 0.002 TYR A 213 ARG 0.002 0.000 ARG D 301 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 426 PHE cc_start: 0.7431 (t80) cc_final: 0.6808 (m-10) REVERT: C 248 TYR cc_start: 0.2841 (OUTLIER) cc_final: 0.2285 (t80) REVERT: C 296 MET cc_start: 0.7157 (mmp) cc_final: 0.6911 (ptm) REVERT: E 223 ILE cc_start: 0.2184 (OUTLIER) cc_final: 0.1461 (mm) outliers start: 17 outliers final: 12 residues processed: 79 average time/residue: 0.1165 time to fit residues: 12.9910 Evaluate side-chains 73 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 441 TYR Chi-restraints excluded: chain C residue 236 CYS Chi-restraints excluded: chain C residue 241 PHE Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 294 PHE Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 223 ILE Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 309 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 25 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 chunk 7 optimal weight: 8.9990 chunk 6 optimal weight: 7.9990 chunk 16 optimal weight: 40.0000 chunk 20 optimal weight: 20.0000 chunk 52 optimal weight: 8.9990 chunk 53 optimal weight: 8.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 479 ASN ** E 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.111015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.092610 restraints weight = 44087.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.091467 restraints weight = 55481.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.091730 restraints weight = 61925.177| |-----------------------------------------------------------------------------| r_work (final): 0.4285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4529 moved from start: 1.4802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 5030 Z= 0.294 Angle : 0.972 14.052 6855 Z= 0.469 Chirality : 0.048 0.410 904 Planarity : 0.007 0.060 798 Dihedral : 6.284 58.009 660 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 24.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.60 % Allowed : 25.30 % Favored : 72.10 % 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: 1.48 (0.34), residues: 616 helix: 1.39 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -2.07 (0.80), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 453 HIS 0.007 0.001 HIS D 300 PHE 0.035 0.002 PHE B 262 TYR 0.022 0.002 TYR A 213 ARG 0.002 0.000 ARG C 277 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 278 MET cc_start: 0.7458 (ppp) cc_final: 0.7153 (ppp) REVERT: A 284 PHE cc_start: 0.9186 (t80) cc_final: 0.8638 (t80) REVERT: A 426 PHE cc_start: 0.7496 (t80) cc_final: 0.6744 (m-10) REVERT: B 218 LEU cc_start: 0.7139 (pp) cc_final: 0.6832 (pp) REVERT: C 248 TYR cc_start: 0.2884 (OUTLIER) cc_final: 0.2375 (t80) REVERT: E 223 ILE cc_start: 0.2950 (OUTLIER) cc_final: 0.2407 (mm) outliers start: 15 outliers final: 13 residues processed: 72 average time/residue: 0.1247 time to fit residues: 12.5464 Evaluate side-chains 72 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 441 TYR Chi-restraints excluded: chain C residue 236 CYS Chi-restraints excluded: chain C residue 241 PHE Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 294 PHE Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 223 ILE Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 309 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 52 optimal weight: 10.0000 chunk 55 optimal weight: 40.0000 chunk 36 optimal weight: 30.0000 chunk 4 optimal weight: 50.0000 chunk 14 optimal weight: 2.9990 chunk 41 optimal weight: 0.0670 chunk 22 optimal weight: 6.9990 chunk 26 optimal weight: 0.0270 chunk 18 optimal weight: 7.9990 chunk 45 optimal weight: 8.9990 chunk 57 optimal weight: 9.9990 overall best weight: 3.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 479 ASN D 300 HIS ** E 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.100507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.087673 restraints weight = 43763.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.085954 restraints weight = 69532.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.084770 restraints weight = 93020.978| |-----------------------------------------------------------------------------| r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4210 moved from start: 1.4893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.194 5030 Z= 0.534 Angle : 1.362 59.197 6855 Z= 0.765 Chirality : 0.051 0.528 904 Planarity : 0.008 0.059 798 Dihedral : 6.382 58.048 660 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 28.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.95 % Allowed : 25.30 % Favored : 71.75 % Cbeta Deviations : 0.16 % 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: 1.42 (0.34), residues: 616 helix: 1.37 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -2.11 (0.77), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 453 HIS 0.008 0.002 HIS D 300 PHE 0.085 0.003 PHE E 472 TYR 0.105 0.004 TYR E 286 ARG 0.001 0.000 ARG A 301 =============================================================================== Job complete usr+sys time: 2012.26 seconds wall clock time: 35 minutes 37.85 seconds (2137.85 seconds total)