Starting phenix.real_space_refine on Wed Sep 17 05:04:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/1oed_1044/09_2025/1oed_1044.cif Found real_map, /net/cci-nas-00/data/ceres_data/1oed_1044/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/1oed_1044/09_2025/1oed_1044.cif" } default_model = "/net/cci-nas-00/data/ceres_data/1oed_1044/09_2025/1oed_1044.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/1oed_1044/09_2025/1oed_1044.map" default_real_map = "/net/cci-nas-00/data/ceres_data/1oed_1044/09_2025/1oed_1044.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.43, per 1000 atoms: 0.29 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: 0.43 Conformation dependent library (CDL) restraints added in 140.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.10 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: 0.72 Time building geometry restraints manager: 0.50 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: 0.050 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.010 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.400 ------------------------------------------------------------------------------- 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= 0.925 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.001 0.000 ARG E 310 TYR 0.014 0.001 TYR B 220 PHE 0.021 0.002 PHE C 247 TRP 0.012 0.005 TRP E 453 HIS 0.006 0.001 HIS B 460 Details of bonding type rmsd covalent geometry : bond 0.01406 ( 5030) covalent geometry : angle 2.28833 ( 6855) hydrogen bonds : bond 0.37982 ( 435) hydrogen bonds : angle 12.12198 ( 1305) *********************** 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 : 0.203 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: 0.4062 (m-80) REVERT: A 284 PHE cc_start: 0.2953 (OUTLIER) cc_final: 0.2444 (t80) REVERT: A 411 LEU cc_start: 0.5778 (OUTLIER) cc_final: 0.4751 (mm) REVERT: C 457 SER cc_start: -0.6578 (OUTLIER) cc_final: -0.7202 (m) REVERT: C 462 THR cc_start: 0.6349 (m) cc_final: 0.5910 (m) REVERT: C 475 MET cc_start: 0.0883 (OUTLIER) cc_final: -0.0570 (mtt) REVERT: C 479 ASN cc_start: -0.2803 (OUTLIER) cc_final: -0.3291 (t0) REVERT: D 243 MET cc_start: 0.3821 (mtt) cc_final: 0.2373 (pmm) REVERT: D 298 THR cc_start: 0.5185 (OUTLIER) cc_final: 0.4851 (m) REVERT: D 302 SER cc_start: 0.6645 (OUTLIER) cc_final: 0.5653 (t) REVERT: E 272 LYS cc_start: 0.5415 (OUTLIER) cc_final: 0.4490 (tttt) REVERT: E 297 ILE cc_start: 0.1827 (OUTLIER) cc_final: 0.1582 (tp) outliers start: 114 outliers final: 46 residues processed: 198 average time/residue: 0.0605 time to fit residues: 15.8799 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 : 0.201 ------------------------------------------------------------------------------- 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 54 optimal weight: 0.0370 chunk 24 optimal weight: 7.9990 chunk 48 optimal weight: 0.7980 chunk 56 optimal weight: 30.0000 chunk 26 optimal weight: 20.0000 chunk 2 optimal weight: 50.0000 chunk 16 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 overall best weight: 4.7664 ------------------------------------------------------------------------------- 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 ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.123138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.106138 restraints weight = 44470.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.106058 restraints weight = 57857.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.105962 restraints weight = 54571.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.105863 restraints weight = 60558.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.105787 restraints weight = 57143.999| |-----------------------------------------------------------------------------| r_work (final): 0.4397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3322 moved from start: 0.6196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 5030 Z= 0.300 Angle : 1.163 12.826 6855 Z= 0.589 Chirality : 0.055 0.256 904 Planarity : 0.009 0.064 798 Dihedral : 13.906 85.148 764 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 33.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 10.75 % Allowed : 16.12 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.72 (0.32), residues: 616 helix: -0.82 (0.21), residues: 563 sheet: None (None), residues: 0 loop : -2.54 (0.80), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 455 TYR 0.034 0.002 TYR C 248 PHE 0.034 0.003 PHE B 286 TRP 0.003 0.001 TRP E 453 HIS 0.008 0.002 HIS D 300 Details of bonding type rmsd covalent geometry : bond 0.00654 ( 5030) covalent geometry : angle 1.16320 ( 6855) hydrogen bonds : bond 0.10026 ( 435) hydrogen bonds : angle 7.08678 ( 1305) *********************** 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 136 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 74 time to evaluate : 0.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 281 ILE cc_start: 0.5016 (mm) cc_final: 0.4443 (mm) REVERT: B 293 PHE cc_start: 0.8131 (OUTLIER) cc_final: 0.7848 (t80) REVERT: B 433 MET cc_start: 0.3960 (mpp) cc_final: 0.2101 (mpp) REVERT: B 440 LEU cc_start: 0.6828 (OUTLIER) cc_final: 0.6582 (tp) REVERT: C 296 MET cc_start: 0.6254 (mmp) cc_final: 0.5805 (ptp) REVERT: D 243 MET cc_start: 0.4739 (mtt) cc_final: 0.3711 (pmm) outliers start: 62 outliers final: 23 residues processed: 120 average time/residue: 0.0592 time to fit residues: 9.6644 Evaluate side-chains 83 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 58 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 289 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 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 278 MET Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 299 HIS Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 243 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 Chi-restraints excluded: chain E residue 454 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 20.0000 chunk 3 optimal weight: 7.9990 chunk 12 optimal weight: 8.9990 chunk 21 optimal weight: 20.0000 chunk 27 optimal weight: 50.0000 chunk 56 optimal weight: 9.9990 chunk 15 optimal weight: 30.0000 chunk 51 optimal weight: 8.9990 chunk 59 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- 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 ** C 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 300 HIS ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4709 r_free = 0.4709 target = 0.119034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.101881 restraints weight = 44868.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.100906 restraints weight = 54642.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.100785 restraints weight = 59796.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.099748 restraints weight = 69874.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.099858 restraints weight = 74592.779| |-----------------------------------------------------------------------------| r_work (final): 0.4331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3635 moved from start: 0.8717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 5030 Z= 0.230 Angle : 1.000 10.905 6855 Z= 0.493 Chirality : 0.049 0.247 904 Planarity : 0.008 0.067 798 Dihedral : 9.202 82.892 682 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 25.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 6.07 % Allowed : 18.54 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.32), residues: 616 helix: -0.31 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -1.63 (0.74), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 301 TYR 0.045 0.002 TYR D 234 PHE 0.023 0.003 PHE C 270 TRP 0.004 0.001 TRP E 453 HIS 0.006 0.002 HIS D 299 Details of bonding type rmsd covalent geometry : bond 0.00533 ( 5030) covalent geometry : angle 0.99953 ( 6855) hydrogen bonds : bond 0.05999 ( 435) hydrogen bonds : angle 5.65666 ( 1305) *********************** 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 105 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 70 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: -0.2280 (tpt) cc_final: -0.2788 (mmm) REVERT: C 296 MET cc_start: 0.6708 (mmp) cc_final: 0.6304 (ptm) REVERT: C 475 MET cc_start: -0.2220 (ptt) cc_final: -0.3491 (mmt) REVERT: D 243 MET cc_start: 0.5141 (OUTLIER) cc_final: 0.4264 (pmm) REVERT: D 435 GLN cc_start: -0.2613 (OUTLIER) cc_final: -0.3018 (mt0) outliers start: 35 outliers final: 13 residues processed: 96 average time/residue: 0.0493 time to fit residues: 6.7875 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 : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 280 ILE Chi-restraints excluded: chain B residue 441 TYR Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 278 MET 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 453 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 13 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 chunk 4 optimal weight: 9.9990 chunk 45 optimal weight: 50.0000 chunk 53 optimal weight: 7.9990 chunk 20 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 chunk 31 optimal weight: 8.9990 chunk 25 optimal weight: 8.9990 chunk 39 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 overall best weight: 8.7990 ------------------------------------------------------------------------------- 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** B 466 ASN C 305 ASN E 225 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.116790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.100285 restraints weight = 44868.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.098688 restraints weight = 55009.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.098685 restraints weight = 64627.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.098685 restraints weight = 64673.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.098685 restraints weight = 64672.822| |-----------------------------------------------------------------------------| r_work (final): 0.4313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3881 moved from start: 1.0563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 5030 Z= 0.204 Angle : 0.925 10.252 6855 Z= 0.454 Chirality : 0.048 0.185 904 Planarity : 0.008 0.068 798 Dihedral : 7.763 73.767 669 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 23.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.68 % Allowed : 20.97 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.33), residues: 616 helix: 0.36 (0.21), residues: 553 sheet: None (None), residues: 0 loop : -1.22 (0.79), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 277 TYR 0.019 0.002 TYR C 248 PHE 0.021 0.003 PHE C 314 TRP 0.002 0.001 TRP E 453 HIS 0.004 0.001 HIS D 300 Details of bonding type rmsd covalent geometry : bond 0.00484 ( 5030) covalent geometry : angle 0.92524 ( 6855) hydrogen bonds : bond 0.04857 ( 435) hydrogen bonds : angle 4.85195 ( 1305) *********************** 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 94 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 67 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: -0.1635 (tpt) cc_final: -0.2066 (mmt) REVERT: B 249 MET cc_start: 0.3380 (mmp) cc_final: 0.3030 (pmm) REVERT: C 294 PHE cc_start: 0.6810 (m-80) cc_final: 0.6518 (m-80) REVERT: C 296 MET cc_start: 0.6756 (mmp) cc_final: 0.6276 (ptm) REVERT: D 243 MET cc_start: 0.5120 (mtt) cc_final: 0.4542 (pmm) outliers start: 27 outliers final: 14 residues processed: 89 average time/residue: 0.0536 time to fit residues: 6.7107 Evaluate side-chains 72 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 432 GLU 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 D residue 278 MET 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 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 14 optimal weight: 40.0000 chunk 58 optimal weight: 40.0000 chunk 8 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 1 optimal weight: 20.0000 chunk 22 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 7 optimal weight: 0.9980 chunk 36 optimal weight: 8.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- 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** ** C 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 479 ASN E 225 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.114899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.097536 restraints weight = 44703.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.097505 restraints weight = 55495.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.097478 restraints weight = 57975.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.097478 restraints weight = 59668.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.097478 restraints weight = 59659.729| |-----------------------------------------------------------------------------| r_work (final): 0.4349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3941 moved from start: 1.1321 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= 0.176 Angle : 0.881 11.005 6855 Z= 0.419 Chirality : 0.045 0.222 904 Planarity : 0.008 0.063 798 Dihedral : 7.204 63.675 667 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 21.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.16 % Allowed : 21.32 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.34), residues: 616 helix: 0.85 (0.22), residues: 555 sheet: None (None), residues: 0 loop : -1.27 (0.79), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 307 TYR 0.011 0.001 TYR B 220 PHE 0.025 0.002 PHE D 256 TRP 0.002 0.001 TRP E 453 HIS 0.003 0.001 HIS D 300 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 5030) covalent geometry : angle 0.88069 ( 6855) hydrogen bonds : bond 0.04254 ( 435) hydrogen bonds : angle 4.48436 ( 1305) *********************** 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 86 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 62 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: A 243 MET cc_start: -0.1483 (tpt) cc_final: -0.1881 (mmt) REVERT: B 249 MET cc_start: 0.3445 (mmp) cc_final: 0.3171 (pmm) REVERT: C 296 MET cc_start: 0.6776 (mmp) cc_final: 0.6347 (ptm) REVERT: C 475 MET cc_start: -0.1920 (ptt) cc_final: -0.3158 (mmt) REVERT: D 243 MET cc_start: 0.5361 (OUTLIER) cc_final: 0.5077 (pmm) REVERT: E 221 PHE cc_start: 0.5764 (OUTLIER) cc_final: 0.5151 (m-80) REVERT: E 286 TYR cc_start: 0.0913 (OUTLIER) cc_final: 0.0665 (m-10) outliers start: 24 outliers final: 9 residues processed: 83 average time/residue: 0.0494 time to fit residues: 5.9479 Evaluate side-chains 65 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.241 ------------------------------------------------------------------------------- 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 241 PHE Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain D residue 243 MET 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 6 optimal weight: 0.9990 chunk 45 optimal weight: 7.9990 chunk 1 optimal weight: 20.0000 chunk 56 optimal weight: 50.0000 chunk 24 optimal weight: 20.0000 chunk 58 optimal weight: 30.0000 chunk 33 optimal weight: 30.0000 chunk 42 optimal weight: 0.5980 chunk 8 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- 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** D 300 HIS E 271 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.100707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.090791 restraints weight = 60978.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.090790 restraints weight = 67871.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.090790 restraints weight = 67873.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.090790 restraints weight = 67873.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.090790 restraints weight = 67873.048| |-----------------------------------------------------------------------------| r_work (final): 0.4247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3903 moved from start: 1.1795 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= 0.171 Angle : 0.883 11.980 6855 Z= 0.420 Chirality : 0.045 0.225 904 Planarity : 0.007 0.064 798 Dihedral : 6.078 59.877 662 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 20.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.81 % Allowed : 20.80 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.34), residues: 616 helix: 1.12 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -1.77 (0.71), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 429 TYR 0.008 0.001 TYR B 220 PHE 0.023 0.002 PHE D 256 TRP 0.003 0.001 TRP E 453 HIS 0.016 0.002 HIS D 300 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 5030) covalent geometry : angle 0.88348 ( 6855) hydrogen bonds : bond 0.04114 ( 435) hydrogen bonds : angle 4.42549 ( 1305) *********************** 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 84 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 62 time to evaluate : 0.204 Fit side-chains revert: symmetry clash REVERT: C 294 PHE cc_start: 0.6283 (m-80) cc_final: 0.5658 (m-80) REVERT: E 221 PHE cc_start: 0.5134 (OUTLIER) cc_final: 0.4923 (m-10) outliers start: 22 outliers final: 13 residues processed: 80 average time/residue: 0.0464 time to fit residues: 5.2653 Evaluate side-chains 71 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.199 ------------------------------------------------------------------------------- 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 441 TYR Chi-restraints excluded: chain C residue 241 PHE Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 281 THR 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 4 optimal weight: 50.0000 chunk 44 optimal weight: 7.9990 chunk 46 optimal weight: 50.0000 chunk 0 optimal weight: 20.0000 chunk 29 optimal weight: 10.0000 chunk 5 optimal weight: 20.0000 chunk 54 optimal weight: 20.0000 chunk 13 optimal weight: 30.0000 chunk 36 optimal weight: 30.0000 chunk 19 optimal weight: 9.9990 chunk 15 optimal weight: 30.0000 overall best weight: 13.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 HIS ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 479 ASN D 300 HIS E 271 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.110180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.092728 restraints weight = 43342.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.091463 restraints weight = 53280.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.091157 restraints weight = 69339.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.091321 restraints weight = 67406.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.091236 restraints weight = 65839.122| |-----------------------------------------------------------------------------| r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4460 moved from start: 1.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 5030 Z= 0.242 Angle : 1.025 11.135 6855 Z= 0.499 Chirality : 0.049 0.190 904 Planarity : 0.008 0.064 798 Dihedral : 6.453 57.741 662 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 25.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.51 % Allowed : 20.80 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.33), residues: 616 helix: 0.72 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -2.36 (0.72), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 301 TYR 0.034 0.002 TYR B 220 PHE 0.026 0.003 PHE B 293 TRP 0.006 0.003 TRP E 453 HIS 0.017 0.002 HIS D 300 Details of bonding type rmsd covalent geometry : bond 0.00566 ( 5030) covalent geometry : angle 1.02527 ( 6855) hydrogen bonds : bond 0.04777 ( 435) hydrogen bonds : angle 4.67681 ( 1305) *********************** 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 97 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 71 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 16 residues processed: 90 average time/residue: 0.0523 time to fit residues: 6.6732 Evaluate side-chains 79 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.196 ------------------------------------------------------------------------------- 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 218 LEU 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 294 PHE Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 273 VAL 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 54 optimal weight: 0.0770 chunk 31 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 chunk 52 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 36 optimal weight: 20.0000 chunk 27 optimal weight: 50.0000 chunk 42 optimal weight: 30.0000 chunk 43 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 overall best weight: 4.8146 ------------------------------------------------------------------------------- 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 ** D 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.110707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.093068 restraints weight = 44377.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.092250 restraints weight = 52441.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.092291 restraints weight = 58835.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.092387 restraints weight = 58080.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.092377 restraints weight = 57648.685| |-----------------------------------------------------------------------------| r_work (final): 0.4298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4397 moved from start: 1.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5030 Z= 0.182 Angle : 0.951 11.500 6855 Z= 0.452 Chirality : 0.047 0.262 904 Planarity : 0.008 0.070 798 Dihedral : 5.849 44.557 660 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 22.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.25 % Allowed : 25.13 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.34), residues: 616 helix: 1.09 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -2.11 (0.74), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 301 TYR 0.034 0.002 TYR A 234 PHE 0.032 0.002 PHE D 256 TRP 0.003 0.001 TRP E 453 HIS 0.006 0.001 HIS B 306 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 5030) covalent geometry : angle 0.95115 ( 6855) hydrogen bonds : bond 0.04264 ( 435) hydrogen bonds : angle 4.48459 ( 1305) *********************** 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 83 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 247 ILE cc_start: 0.0119 (OUTLIER) cc_final: -0.0081 (mm) REVERT: B 218 LEU cc_start: 0.7952 (tt) cc_final: 0.7644 (tp) REVERT: C 248 TYR cc_start: 0.2861 (OUTLIER) cc_final: 0.2281 (t80) REVERT: E 291 MET cc_start: 0.5307 (mmt) cc_final: 0.5000 (mmt) outliers start: 13 outliers final: 9 residues processed: 81 average time/residue: 0.0500 time to fit residues: 5.8503 Evaluate side-chains 74 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.238 ------------------------------------------------------------------------------- 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 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 D residue 235 LEU Chi-restraints excluded: chain D residue 281 THR 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 42 optimal weight: 30.0000 chunk 26 optimal weight: 40.0000 chunk 47 optimal weight: 40.0000 chunk 33 optimal weight: 0.3980 chunk 59 optimal weight: 9.9990 chunk 0 optimal weight: 40.0000 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 19 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 30 optimal weight: 20.0000 overall best weight: 4.8788 ------------------------------------------------------------------------------- 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 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 477 ASN ** D 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.110831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.093111 restraints weight = 43853.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.092882 restraints weight = 51878.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.091362 restraints weight = 65566.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.091310 restraints weight = 68122.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.091881 restraints weight = 67149.525| |-----------------------------------------------------------------------------| r_work (final): 0.4283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4473 moved from start: 1.4584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5030 Z= 0.176 Angle : 0.988 16.967 6855 Z= 0.462 Chirality : 0.049 0.525 904 Planarity : 0.008 0.071 798 Dihedral : 5.654 47.853 660 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 22.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.29 % Allowed : 24.78 % Favored : 71.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.34), residues: 616 helix: 1.22 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -2.08 (0.70), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 282 TYR 0.039 0.002 TYR A 234 PHE 0.032 0.002 PHE D 256 TRP 0.003 0.001 TRP E 453 HIS 0.006 0.001 HIS B 306 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 5030) covalent geometry : angle 0.98839 ( 6855) hydrogen bonds : bond 0.04285 ( 435) hydrogen bonds : angle 4.40564 ( 1305) *********************** 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 82 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 248 TYR cc_start: 0.2771 (OUTLIER) cc_final: 0.2287 (t80) REVERT: D 278 MET cc_start: 0.6092 (ppp) cc_final: 0.5515 (ppp) REVERT: E 221 PHE cc_start: 0.6028 (OUTLIER) cc_final: 0.5706 (m-10) outliers start: 19 outliers final: 10 residues processed: 78 average time/residue: 0.0524 time to fit residues: 5.8304 Evaluate side-chains 72 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 253 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 248 TYR Chi-restraints excluded: chain C residue 256 LYS Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 281 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 7 optimal weight: 40.0000 chunk 31 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 10 optimal weight: 50.0000 chunk 22 optimal weight: 40.0000 chunk 33 optimal weight: 10.0000 chunk 24 optimal weight: 0.6980 chunk 8 optimal weight: 20.0000 chunk 26 optimal weight: 30.0000 chunk 5 optimal weight: 30.0000 chunk 47 optimal weight: 6.9990 overall best weight: 6.3390 ------------------------------------------------------------------------------- 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 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 300 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 = 0.4659 r_free = 0.4659 target = 0.110923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.093139 restraints weight = 43960.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.092068 restraints weight = 51076.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.091983 restraints weight = 60424.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.092014 restraints weight = 59375.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.091985 restraints weight = 61171.771| |-----------------------------------------------------------------------------| r_work (final): 0.4248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4517 moved from start: 1.5208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5030 Z= 0.183 Angle : 1.005 14.811 6855 Z= 0.472 Chirality : 0.050 0.440 904 Planarity : 0.008 0.072 798 Dihedral : 5.678 50.603 658 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 23.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.91 % Allowed : 26.34 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.34), residues: 616 helix: 1.23 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -2.46 (0.68), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 437 TYR 0.035 0.002 TYR A 234 PHE 0.025 0.002 PHE B 286 TRP 0.005 0.002 TRP E 453 HIS 0.007 0.001 HIS B 306 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 5030) covalent geometry : angle 1.00520 ( 6855) hydrogen bonds : bond 0.04484 ( 435) hydrogen bonds : angle 4.48472 ( 1305) ********************** 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 76 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.179 Fit side-chains revert: symmetry clash REVERT: B 440 LEU cc_start: 0.8246 (mm) cc_final: 0.7402 (tp) REVERT: C 248 TYR cc_start: 0.3013 (OUTLIER) cc_final: 0.2243 (t80) REVERT: C 458 MET cc_start: 0.5714 (mmp) cc_final: 0.5430 (mmt) REVERT: D 278 MET cc_start: 0.6268 (ppp) cc_final: 0.5770 (ppp) REVERT: E 221 PHE cc_start: 0.5903 (OUTLIER) cc_final: 0.5652 (m-10) REVERT: E 267 PHE cc_start: 0.7618 (t80) cc_final: 0.7063 (t80) REVERT: E 272 LYS cc_start: 0.8991 (mttt) cc_final: 0.8714 (ptpt) REVERT: E 459 PHE cc_start: 0.7843 (t80) cc_final: 0.7507 (t80) outliers start: 11 outliers final: 8 residues processed: 74 average time/residue: 0.0480 time to fit residues: 5.0720 Evaluate side-chains 71 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 248 TYR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 281 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 24 optimal weight: 0.1980 chunk 13 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 14 optimal weight: 20.0000 chunk 0 optimal weight: 50.0000 chunk 30 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 overall best weight: 3.6388 ------------------------------------------------------------------------------- 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 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 300 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 = 0.4673 r_free = 0.4673 target = 0.111613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.092677 restraints weight = 43527.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.091812 restraints weight = 55305.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.091749 restraints weight = 62574.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.091588 restraints weight = 63422.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.091654 restraints weight = 62983.862| |-----------------------------------------------------------------------------| r_work (final): 0.4246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4567 moved from start: 1.5525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5030 Z= 0.180 Angle : 1.015 15.222 6855 Z= 0.479 Chirality : 0.049 0.386 904 Planarity : 0.007 0.073 798 Dihedral : 5.744 53.773 658 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 21.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.91 % Allowed : 27.38 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.34), residues: 616 helix: 1.27 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -2.57 (0.69), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 301 TYR 0.036 0.002 TYR A 234 PHE 0.042 0.002 PHE B 293 TRP 0.004 0.001 TRP E 453 HIS 0.006 0.001 HIS B 306 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 5030) covalent geometry : angle 1.01481 ( 6855) hydrogen bonds : bond 0.04381 ( 435) hydrogen bonds : angle 4.41870 ( 1305) =============================================================================== Job complete usr+sys time: 1208.54 seconds wall clock time: 21 minutes 34.27 seconds (1294.27 seconds total)