Starting phenix.real_space_refine on Wed Aug 5 02:55:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jew_36201/08_2026/8jew_36201.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jew_36201/08_2026/8jew_36201.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jew_36201/08_2026/8jew_36201.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jew_36201/08_2026/8jew_36201.map" model { file = "/net/cci-nas-00/data/ceres_data/8jew_36201/08_2026/8jew_36201.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jew_36201/08_2026/8jew_36201.cif" } resolution = 2.49 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= 0.001 sd= 0.014 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 58 5.16 5 Na 4 4.78 5 C 5504 2.51 5 N 1246 2.21 5 O 1470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8284 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3881 Classifications: {'peptide': 512} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 478} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 261 Unusual residues: {' NA': 2, 'ASC': 1, 'AV0': 2, 'CLR': 2, 'LBN': 1, 'NAG': 1, 'PLM': 1} Classifications: {'undetermined': 10, 'water': 3} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'LBN:plan-3': 1, 'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Restraints were copied for chains: B Time building chain proxies: 3.14, per 1000 atoms: 0.38 Number of scatterers: 8284 At special positions: 0 Unit cell: (94.62, 108.564, 77.688, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 58 16.00 P 2 15.00 Na 4 11.00 O 1470 8.00 N 1246 7.00 C 5504 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 315.3 milliseconds 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1852 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 2 sheets defined 74.4% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 40 through 60 removed outlier: 3.720A pdb=" N LEU A 46 " --> pdb=" O TYR A 42 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLY A 58 " --> pdb=" O THR A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 70 removed outlier: 3.775A pdb=" N PHE A 64 " --> pdb=" O ILE A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 101 Processing helix chain 'A' and resid 111 through 123 removed outlier: 3.860A pdb=" N LEU A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL A 116 " --> pdb=" O PHE A 112 " (cutoff:3.500A) Proline residue: A 117 - end of helix Processing helix chain 'A' and resid 124 through 128 Processing helix chain 'A' and resid 131 through 136 removed outlier: 3.559A pdb=" N ILE A 135 " --> pdb=" O PRO A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 173 Proline residue: A 151 - end of helix removed outlier: 3.562A pdb=" N GLU A 155 " --> pdb=" O PRO A 151 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL A 166 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 180 removed outlier: 3.894A pdb=" N LEU A 180 " --> pdb=" O PRO A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 198 Proline residue: A 190 - end of helix Processing helix chain 'A' and resid 199 through 208 Processing helix chain 'A' and resid 210 through 227 Processing helix chain 'A' and resid 255 through 274 Processing helix chain 'A' and resid 285 through 289 Processing helix chain 'A' and resid 317 through 346 removed outlier: 3.895A pdb=" N SER A 326 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA A 327 " --> pdb=" O GLY A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 374 Processing helix chain 'A' and resid 382 through 393 removed outlier: 3.682A pdb=" N ILE A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 413 removed outlier: 3.715A pdb=" N VAL A 400 " --> pdb=" O SER A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 421 Processing helix chain 'A' and resid 424 through 445 removed outlier: 3.540A pdb=" N THR A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 450 Processing helix chain 'A' and resid 454 through 478 Proline residue: A 472 - end of helix Processing helix chain 'A' and resid 479 through 482 removed outlier: 4.509A pdb=" N ILE A 482 " --> pdb=" O PRO A 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 479 through 482' Processing helix chain 'A' and resid 486 through 498 Processing helix chain 'A' and resid 499 through 515 Processing helix chain 'A' and resid 541 through 545 Processing helix chain 'A' and resid 549 through 554 Processing helix chain 'A' and resid 556 through 561 Processing helix chain 'B' and resid 40 through 60 removed outlier: 3.720A pdb=" N LEU B 46 " --> pdb=" O TYR B 42 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLY B 58 " --> pdb=" O THR B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 70 removed outlier: 3.775A pdb=" N PHE B 64 " --> pdb=" O ILE B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 101 Processing helix chain 'B' and resid 111 through 123 removed outlier: 3.860A pdb=" N LEU B 115 " --> pdb=" O ALA B 111 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL B 116 " --> pdb=" O PHE B 112 " (cutoff:3.500A) Proline residue: B 117 - end of helix Processing helix chain 'B' and resid 124 through 128 Processing helix chain 'B' and resid 131 through 136 removed outlier: 3.559A pdb=" N ILE B 135 " --> pdb=" O PRO B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 173 Proline residue: B 151 - end of helix removed outlier: 3.562A pdb=" N GLU B 155 " --> pdb=" O PRO B 151 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL B 166 " --> pdb=" O VAL B 162 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU B 167 " --> pdb=" O SER B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 180 removed outlier: 3.894A pdb=" N LEU B 180 " --> pdb=" O PRO B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 198 Proline residue: B 190 - end of helix Processing helix chain 'B' and resid 199 through 208 Processing helix chain 'B' and resid 210 through 227 Processing helix chain 'B' and resid 255 through 274 Processing helix chain 'B' and resid 285 through 289 Processing helix chain 'B' and resid 317 through 346 removed outlier: 3.895A pdb=" N SER B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA B 327 " --> pdb=" O GLY B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 374 Processing helix chain 'B' and resid 382 through 393 removed outlier: 3.682A pdb=" N ILE B 386 " --> pdb=" O SER B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 413 removed outlier: 3.715A pdb=" N VAL B 400 " --> pdb=" O SER B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 421 Processing helix chain 'B' and resid 424 through 445 removed outlier: 3.540A pdb=" N THR B 434 " --> pdb=" O GLY B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 450 Processing helix chain 'B' and resid 454 through 478 Proline residue: B 472 - end of helix Processing helix chain 'B' and resid 479 through 482 removed outlier: 4.509A pdb=" N ILE B 482 " --> pdb=" O PRO B 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 479 through 482' Processing helix chain 'B' and resid 486 through 498 Processing helix chain 'B' and resid 499 through 515 Processing helix chain 'B' and resid 541 through 545 Processing helix chain 'B' and resid 549 through 554 Processing helix chain 'B' and resid 556 through 561 Processing sheet with id=1, first strand: chain 'A' and resid 108 through 110 Processing sheet with id=2, first strand: chain 'B' and resid 108 through 110 506 hydrogen bonds defined for protein. 1452 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: 0.97 Time building geometry restraints manager: 1.12 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: 1206 1.31 - 1.44: 2212 1.44 - 1.58: 4978 1.58 - 1.71: 4 1.71 - 1.84: 88 Bond restraints: 8488 Sorted by residual: bond pdb=" C TYR B 474 " pdb=" O TYR B 474 " ideal model delta sigma weight residual 1.236 1.293 -0.057 1.15e-02 7.56e+03 2.45e+01 bond pdb=" C TYR A 474 " pdb=" O TYR A 474 " ideal model delta sigma weight residual 1.236 1.293 -0.057 1.15e-02 7.56e+03 2.45e+01 bond pdb=" C PRO A 301 " pdb=" O PRO A 301 " ideal model delta sigma weight residual 1.233 1.179 0.054 1.19e-02 7.06e+03 2.06e+01 bond pdb=" C PRO B 301 " pdb=" O PRO B 301 " ideal model delta sigma weight residual 1.233 1.179 0.054 1.19e-02 7.06e+03 2.06e+01 bond pdb=" C GLN B 287 " pdb=" O GLN B 287 " ideal model delta sigma weight residual 1.236 1.176 0.060 1.35e-02 5.49e+03 1.98e+01 ... (remaining 8483 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 8676 2.07 - 4.14: 2672 4.14 - 6.21: 224 6.21 - 8.29: 12 8.29 - 10.36: 4 Bond angle restraints: 11588 Sorted by residual: angle pdb=" N TYR A 42 " pdb=" CA TYR A 42 " pdb=" C TYR A 42 " ideal model delta sigma weight residual 111.71 106.27 5.44 1.15e+00 7.56e-01 2.24e+01 angle pdb=" N TYR B 42 " pdb=" CA TYR B 42 " pdb=" C TYR B 42 " ideal model delta sigma weight residual 111.71 106.27 5.44 1.15e+00 7.56e-01 2.24e+01 angle pdb=" CA ILE A 218 " pdb=" C ILE A 218 " pdb=" O ILE A 218 " ideal model delta sigma weight residual 121.17 116.22 4.95 1.06e+00 8.90e-01 2.18e+01 angle pdb=" CA ILE B 218 " pdb=" C ILE B 218 " pdb=" O ILE B 218 " ideal model delta sigma weight residual 121.17 116.22 4.95 1.06e+00 8.90e-01 2.18e+01 angle pdb=" O ILE A 218 " pdb=" C ILE A 218 " pdb=" N LEU A 219 " ideal model delta sigma weight residual 121.91 126.38 -4.47 9.80e-01 1.04e+00 2.08e+01 ... (remaining 11583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.32: 5262 28.32 - 56.64: 200 56.64 - 84.95: 32 84.95 - 113.27: 0 113.27 - 141.59: 8 Dihedral angle restraints: 5502 sinusoidal: 2602 harmonic: 2900 Sorted by residual: dihedral pdb=" C1 LBN B 605 " pdb=" O1 LBN B 605 " pdb=" P1 LBN B 605 " pdb=" O3 LBN B 605 " ideal model delta sinusoidal sigma weight residual -84.60 56.99 -141.59 1 3.00e+01 1.11e-03 1.90e+01 dihedral pdb=" C1 LBN A 605 " pdb=" O1 LBN A 605 " pdb=" P1 LBN A 605 " pdb=" O3 LBN A 605 " ideal model delta sinusoidal sigma weight residual -84.60 56.99 -141.59 1 3.00e+01 1.11e-03 1.90e+01 dihedral pdb=" O5 LBN A 605 " pdb=" C2 LBN A 605 " pdb=" C3 LBN A 605 " pdb=" O7 LBN A 605 " ideal model delta sinusoidal sigma weight residual 62.67 -60.77 123.44 1 3.00e+01 1.11e-03 1.65e+01 ... (remaining 5499 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 630 0.049 - 0.098: 436 0.098 - 0.147: 232 0.147 - 0.196: 100 0.196 - 0.244: 24 Chirality restraints: 1422 Sorted by residual: chirality pdb=" CA PRO B 563 " pdb=" N PRO B 563 " pdb=" C PRO B 563 " pdb=" CB PRO B 563 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CA PRO A 563 " pdb=" N PRO A 563 " pdb=" C PRO A 563 " pdb=" CB PRO A 563 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CA TRP B 149 " pdb=" N TRP B 149 " pdb=" C TRP B 149 " pdb=" CB TRP B 149 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.38e+00 ... (remaining 1419 not shown) Planarity restraints: 1352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 609 " -0.056 2.00e-02 2.50e+03 4.63e-02 2.67e+01 pdb=" C7 NAG A 609 " 0.006 2.00e-02 2.50e+03 pdb=" C8 NAG A 609 " -0.040 2.00e-02 2.50e+03 pdb=" N2 NAG A 609 " 0.076 2.00e-02 2.50e+03 pdb=" O7 NAG A 609 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 609 " -0.056 2.00e-02 2.50e+03 4.63e-02 2.67e+01 pdb=" C7 NAG B 609 " 0.006 2.00e-02 2.50e+03 pdb=" C8 NAG B 609 " -0.040 2.00e-02 2.50e+03 pdb=" N2 NAG B 609 " 0.076 2.00e-02 2.50e+03 pdb=" O7 NAG B 609 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 311 " -0.027 2.00e-02 2.50e+03 2.91e-02 2.11e+01 pdb=" CG TRP A 311 " 0.000 2.00e-02 2.50e+03 pdb=" CD1 TRP A 311 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP A 311 " 0.058 2.00e-02 2.50e+03 pdb=" NE1 TRP A 311 " -0.029 2.00e-02 2.50e+03 pdb=" CE2 TRP A 311 " 0.031 2.00e-02 2.50e+03 pdb=" CE3 TRP A 311 " 0.025 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 311 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 311 " -0.039 2.00e-02 2.50e+03 pdb=" CH2 TRP A 311 " -0.019 2.00e-02 2.50e+03 ... (remaining 1349 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 32 2.53 - 3.12: 6304 3.12 - 3.71: 13560 3.71 - 4.31: 19920 4.31 - 4.90: 32382 Nonbonded interactions: 72198 Sorted by model distance: nonbonded pdb=" OD2 ASP A 338 " pdb="NA NA A 602 " model vdw 1.932 2.470 nonbonded pdb=" OD2 ASP B 338 " pdb="NA NA B 602 " model vdw 1.932 2.470 nonbonded pdb=" ND2 ASN B 144 " pdb=" C1 NAG B 609 " model vdw 2.059 3.550 nonbonded pdb=" ND2 ASN A 144 " pdb=" C1 NAG A 609 " model vdw 2.059 3.550 nonbonded pdb=" OAI AV0 A 604 " pdb=" OH TYR B 474 " model vdw 2.228 3.040 ... (remaining 72193 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.120 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: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.910 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 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 : 0.015 0.069 8490 Z= 1.059 Angle : 1.791 10.357 11588 Z= 1.295 Chirality : 0.085 0.244 1422 Planarity : 0.014 0.117 1352 Dihedral : 15.566 141.589 3650 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.48 % Allowed : 12.38 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.24), residues: 1012 helix: -0.06 (0.18), residues: 664 sheet: None (None), residues: 0 loop : -0.56 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.003 ARG B 555 TYR 0.043 0.009 TYR B 474 PHE 0.050 0.010 PHE A 459 TRP 0.058 0.012 TRP A 311 HIS 0.014 0.005 HIS A 210 Details of bonding type rmsd/Z covalent geometry : bond 0.01479 / 1.06 ( 8488) covalent geometry : angle 1.79076 / 1.29 (11588) hydrogen bonds : bond 0.18082 / 12.17 ( 506) hydrogen bonds : angle 7.15593 / 4.96 ( 1452) Misc. bond : bond 0.01839 / 0.92 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 144 time to evaluate : 0.315 Fit side-chains REVERT: A 78 MET cc_start: 0.8861 (tmt) cc_final: 0.8390 (tmt) REVERT: A 99 THR cc_start: 0.8314 (t) cc_final: 0.8100 (p) REVERT: A 119 LYS cc_start: 0.7518 (pttp) cc_final: 0.7301 (mtmm) REVERT: A 161 MET cc_start: 0.8740 (mtp) cc_final: 0.8324 (mtm) REVERT: A 172 LEU cc_start: 0.8139 (tp) cc_final: 0.7673 (mt) REVERT: A 201 GLN cc_start: 0.8477 (tp40) cc_final: 0.7092 (mt0) REVERT: A 251 ILE cc_start: 0.7110 (tt) cc_final: 0.6770 (pt) REVERT: A 334 GLU cc_start: 0.8383 (tt0) cc_final: 0.8141 (tt0) REVERT: A 381 SER cc_start: 0.8036 (m) cc_final: 0.7664 (p) REVERT: A 476 GLU cc_start: 0.7849 (tp30) cc_final: 0.7310 (mm-30) REVERT: A 500 GLU cc_start: 0.7758 (mp0) cc_final: 0.7470 (mp0) REVERT: A 550 MET cc_start: 0.3349 (tpt) cc_final: 0.3060 (tpt) REVERT: B 78 MET cc_start: 0.8857 (tmt) cc_final: 0.8387 (tmt) REVERT: B 99 THR cc_start: 0.8316 (t) cc_final: 0.8101 (p) REVERT: B 119 LYS cc_start: 0.7520 (pttp) cc_final: 0.7302 (mtmm) REVERT: B 161 MET cc_start: 0.8740 (mtp) cc_final: 0.8323 (mtm) REVERT: B 172 LEU cc_start: 0.8133 (tp) cc_final: 0.7668 (mt) REVERT: B 201 GLN cc_start: 0.8477 (tp40) cc_final: 0.7093 (mt0) REVERT: B 251 ILE cc_start: 0.7110 (tt) cc_final: 0.6772 (pt) REVERT: B 334 GLU cc_start: 0.8380 (tt0) cc_final: 0.8139 (tt0) REVERT: B 381 SER cc_start: 0.8037 (m) cc_final: 0.7664 (p) REVERT: B 476 GLU cc_start: 0.7850 (tp30) cc_final: 0.7312 (mm-30) REVERT: B 500 GLU cc_start: 0.7761 (mp0) cc_final: 0.7473 (mp0) REVERT: B 550 MET cc_start: 0.3351 (tpt) cc_final: 0.3063 (tpt) outliers start: 4 outliers final: 0 residues processed: 148 average time/residue: 0.4631 time to fit residues: 73.1600 Evaluate side-chains 120 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 0.0670 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 GLN ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 ASN B 50 GLN ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.149105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.111375 restraints weight = 7869.928| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.28 r_work: 0.3080 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8490 Z= 0.156 Angle : 0.661 8.280 11588 Z= 0.327 Chirality : 0.043 0.167 1422 Planarity : 0.005 0.033 1352 Dihedral : 12.740 128.545 1940 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.19 % Allowed : 14.29 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.26), residues: 1012 helix: 1.49 (0.19), residues: 662 sheet: None (None), residues: 0 loop : 0.30 (0.36), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 456 TYR 0.010 0.002 TYR A 474 PHE 0.019 0.002 PHE B 558 TRP 0.017 0.002 TRP A 149 HIS 0.003 0.001 HIS A 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 ( 8488) covalent geometry : angle 0.66135 / 0.33 (11588) hydrogen bonds : bond 0.05661 / 4.05 ( 506) hydrogen bonds : angle 5.16115 / 3.69 ( 1452) Misc. bond : bond 0.00021 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 0.191 Fit side-chains REVERT: A 78 MET cc_start: 0.8784 (tmt) cc_final: 0.8337 (tmt) REVERT: A 161 MET cc_start: 0.9036 (mtp) cc_final: 0.8658 (mtm) REVERT: A 172 LEU cc_start: 0.8567 (tp) cc_final: 0.8143 (mt) REVERT: A 251 ILE cc_start: 0.7652 (OUTLIER) cc_final: 0.7195 (pt) REVERT: A 550 MET cc_start: 0.4791 (tpt) cc_final: 0.4237 (tpt) REVERT: B 78 MET cc_start: 0.8781 (tmt) cc_final: 0.8337 (tmt) REVERT: B 161 MET cc_start: 0.9038 (mtp) cc_final: 0.8661 (mtm) REVERT: B 172 LEU cc_start: 0.8563 (tp) cc_final: 0.8147 (mt) REVERT: B 251 ILE cc_start: 0.7659 (OUTLIER) cc_final: 0.7202 (pt) REVERT: B 550 MET cc_start: 0.4781 (tpt) cc_final: 0.4230 (tpt) outliers start: 10 outliers final: 2 residues processed: 132 average time/residue: 0.5195 time to fit residues: 73.2596 Evaluate side-chains 112 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 108 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 407 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 96 optimal weight: 9.9990 chunk 26 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 57 optimal weight: 9.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 GLN ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 GLN ** B 76 GLN ** 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 = 0.3654 r_free = 0.3654 target = 0.150114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.112568 restraints weight = 7861.889| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.28 r_work: 0.3057 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8490 Z= 0.139 Angle : 0.611 7.500 11588 Z= 0.298 Chirality : 0.042 0.139 1422 Planarity : 0.005 0.039 1352 Dihedral : 12.571 132.618 1940 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.62 % Allowed : 14.05 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.26), residues: 1012 helix: 1.73 (0.19), residues: 676 sheet: None (None), residues: 0 loop : 0.84 (0.37), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 456 TYR 0.009 0.001 TYR B 474 PHE 0.016 0.002 PHE A 558 TRP 0.015 0.001 TRP A 149 HIS 0.003 0.001 HIS B 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 ( 8488) covalent geometry : angle 0.61055 / 0.30 (11588) hydrogen bonds : bond 0.05128 / 3.67 ( 506) hydrogen bonds : angle 4.87663 / 3.50 ( 1452) Misc. bond : bond 0.00020 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.270 Fit side-chains REVERT: A 78 MET cc_start: 0.8772 (tmt) cc_final: 0.8347 (tmt) REVERT: A 161 MET cc_start: 0.9033 (mtp) cc_final: 0.8614 (mtm) REVERT: A 172 LEU cc_start: 0.8485 (tp) cc_final: 0.8090 (mt) REVERT: A 251 ILE cc_start: 0.7713 (OUTLIER) cc_final: 0.7253 (pt) REVERT: A 550 MET cc_start: 0.4859 (tpt) cc_final: 0.4444 (tpt) REVERT: B 78 MET cc_start: 0.8764 (tmt) cc_final: 0.8339 (tmt) REVERT: B 161 MET cc_start: 0.9040 (mtp) cc_final: 0.8621 (mtm) REVERT: B 172 LEU cc_start: 0.8480 (tp) cc_final: 0.8089 (mt) REVERT: B 251 ILE cc_start: 0.7708 (OUTLIER) cc_final: 0.7249 (pt) REVERT: B 550 MET cc_start: 0.4860 (tpt) cc_final: 0.4448 (tpt) outliers start: 22 outliers final: 8 residues processed: 130 average time/residue: 0.5160 time to fit residues: 71.5662 Evaluate side-chains 121 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 489 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 92 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 GLN ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 GLN ** B 76 GLN ** 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 = 0.3648 r_free = 0.3648 target = 0.149302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.114189 restraints weight = 8191.751| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.18 r_work: 0.3027 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8490 Z= 0.217 Angle : 0.715 8.042 11588 Z= 0.351 Chirality : 0.047 0.179 1422 Planarity : 0.006 0.041 1352 Dihedral : 13.318 133.336 1940 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.86 % Allowed : 14.76 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.26), residues: 1012 helix: 1.38 (0.19), residues: 664 sheet: None (None), residues: 0 loop : 0.74 (0.37), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 456 TYR 0.015 0.002 TYR A 42 PHE 0.023 0.003 PHE B 200 TRP 0.016 0.002 TRP A 149 HIS 0.003 0.001 HIS A 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.22 ( 8488) covalent geometry : angle 0.71475 / 0.35 (11588) hydrogen bonds : bond 0.06278 / 4.48 ( 506) hydrogen bonds : angle 5.15011 / 3.70 ( 1452) Misc. bond : bond 0.00038 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.307 Fit side-chains REVERT: A 78 MET cc_start: 0.8801 (tmt) cc_final: 0.8448 (tmt) REVERT: A 161 MET cc_start: 0.9062 (mtp) cc_final: 0.8690 (mtm) REVERT: A 172 LEU cc_start: 0.8556 (tp) cc_final: 0.8151 (mt) REVERT: A 251 ILE cc_start: 0.7624 (OUTLIER) cc_final: 0.7145 (pt) REVERT: A 550 MET cc_start: 0.5083 (tpt) cc_final: 0.4355 (tpt) REVERT: B 78 MET cc_start: 0.8801 (tmt) cc_final: 0.8453 (tmt) REVERT: B 161 MET cc_start: 0.9068 (mtp) cc_final: 0.8697 (mtm) REVERT: B 172 LEU cc_start: 0.8553 (tp) cc_final: 0.8154 (mt) REVERT: B 251 ILE cc_start: 0.7626 (OUTLIER) cc_final: 0.7145 (pt) REVERT: B 550 MET cc_start: 0.5078 (tpt) cc_final: 0.4355 (tpt) outliers start: 24 outliers final: 16 residues processed: 126 average time/residue: 0.4590 time to fit residues: 62.0985 Evaluate side-chains 126 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 344 ARG Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 344 ARG Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 489 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 7 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 22 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 67 optimal weight: 7.9990 chunk 29 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 GLN B 50 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.152386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.117246 restraints weight = 8202.623| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.22 r_work: 0.3110 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8490 Z= 0.119 Angle : 0.589 9.122 11588 Z= 0.281 Chirality : 0.041 0.138 1422 Planarity : 0.005 0.042 1352 Dihedral : 12.571 134.708 1940 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.86 % Allowed : 15.48 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.27), residues: 1012 helix: 1.79 (0.19), residues: 678 sheet: None (None), residues: 0 loop : 1.09 (0.38), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 456 TYR 0.007 0.001 TYR B 474 PHE 0.015 0.002 PHE A 361 TRP 0.013 0.001 TRP A 149 HIS 0.002 0.000 HIS A 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 ( 8488) covalent geometry : angle 0.58904 / 0.28 (11588) hydrogen bonds : bond 0.04540 / 3.25 ( 506) hydrogen bonds : angle 4.76190 / 3.43 ( 1452) Misc. bond : bond 0.00013 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 0.309 Fit side-chains REVERT: A 161 MET cc_start: 0.8989 (mtp) cc_final: 0.8574 (mtm) REVERT: A 172 LEU cc_start: 0.8401 (tp) cc_final: 0.8030 (mt) REVERT: A 251 ILE cc_start: 0.7558 (OUTLIER) cc_final: 0.7197 (pt) REVERT: A 550 MET cc_start: 0.5097 (tpt) cc_final: 0.4314 (tpt) REVERT: B 161 MET cc_start: 0.8994 (mtp) cc_final: 0.8578 (mtm) REVERT: B 172 LEU cc_start: 0.8403 (tp) cc_final: 0.8027 (mt) REVERT: B 251 ILE cc_start: 0.7549 (OUTLIER) cc_final: 0.7189 (pt) REVERT: B 550 MET cc_start: 0.5091 (tpt) cc_final: 0.4313 (tpt) outliers start: 24 outliers final: 10 residues processed: 122 average time/residue: 0.4691 time to fit residues: 61.5572 Evaluate side-chains 120 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 407 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 93 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 chunk 8 optimal weight: 0.8980 chunk 73 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 99 optimal weight: 8.9990 chunk 57 optimal weight: 20.0000 chunk 17 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 59 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.148143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.110880 restraints weight = 7883.305| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.27 r_work: 0.3025 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8490 Z= 0.179 Angle : 0.665 7.698 11588 Z= 0.322 Chirality : 0.044 0.161 1422 Planarity : 0.005 0.041 1352 Dihedral : 12.877 134.216 1940 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.14 % Allowed : 16.67 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.26), residues: 1012 helix: 1.61 (0.19), residues: 666 sheet: None (None), residues: 0 loop : 1.08 (0.37), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 456 TYR 0.013 0.002 TYR A 42 PHE 0.020 0.002 PHE B 459 TRP 0.015 0.002 TRP B 149 HIS 0.003 0.001 HIS A 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 ( 8488) covalent geometry : angle 0.66481 / 0.32 (11588) hydrogen bonds : bond 0.05638 / 4.03 ( 506) hydrogen bonds : angle 4.96550 / 3.57 ( 1452) Misc. bond : bond 0.00023 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.278 Fit side-chains REVERT: A 161 MET cc_start: 0.9048 (mtp) cc_final: 0.8626 (mtm) REVERT: A 172 LEU cc_start: 0.8546 (tp) cc_final: 0.8113 (mt) REVERT: A 251 ILE cc_start: 0.7599 (OUTLIER) cc_final: 0.7230 (pt) REVERT: A 550 MET cc_start: 0.4919 (tpt) cc_final: 0.4077 (tpt) REVERT: B 161 MET cc_start: 0.9054 (mtp) cc_final: 0.8634 (mtm) REVERT: B 172 LEU cc_start: 0.8542 (tp) cc_final: 0.8113 (mt) REVERT: B 251 ILE cc_start: 0.7596 (OUTLIER) cc_final: 0.7229 (pt) REVERT: B 550 MET cc_start: 0.4928 (tpt) cc_final: 0.4088 (tpt) outliers start: 18 outliers final: 10 residues processed: 114 average time/residue: 0.5540 time to fit residues: 67.5266 Evaluate side-chains 122 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 407 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 43 optimal weight: 9.9990 chunk 50 optimal weight: 0.8980 chunk 7 optimal weight: 9.9990 chunk 91 optimal weight: 0.0870 chunk 37 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 overall best weight: 2.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.150171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.115563 restraints weight = 8220.955| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.17 r_work: 0.3054 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8490 Z= 0.160 Angle : 0.642 7.667 11588 Z= 0.311 Chirality : 0.043 0.152 1422 Planarity : 0.005 0.041 1352 Dihedral : 12.804 133.734 1940 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.86 % Allowed : 15.95 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.26), residues: 1012 helix: 1.54 (0.19), residues: 678 sheet: None (None), residues: 0 loop : 1.16 (0.38), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 456 TYR 0.011 0.002 TYR B 42 PHE 0.017 0.002 PHE A 459 TRP 0.015 0.002 TRP A 149 HIS 0.002 0.001 HIS A 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 ( 8488) covalent geometry : angle 0.64158 / 0.31 (11588) hydrogen bonds : bond 0.05346 / 3.82 ( 506) hydrogen bonds : angle 4.91517 / 3.53 ( 1452) Misc. bond : bond 0.00023 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.210 Fit side-chains REVERT: A 161 MET cc_start: 0.9038 (mtp) cc_final: 0.8623 (mtm) REVERT: A 172 LEU cc_start: 0.8519 (tp) cc_final: 0.8115 (mt) REVERT: A 251 ILE cc_start: 0.7593 (OUTLIER) cc_final: 0.7243 (pt) REVERT: A 550 MET cc_start: 0.4984 (tpt) cc_final: 0.4117 (tpt) REVERT: B 161 MET cc_start: 0.9040 (mtp) cc_final: 0.8626 (mtm) REVERT: B 172 LEU cc_start: 0.8515 (tp) cc_final: 0.8114 (mt) REVERT: B 251 ILE cc_start: 0.7593 (OUTLIER) cc_final: 0.7241 (pt) REVERT: B 550 MET cc_start: 0.4981 (tpt) cc_final: 0.4114 (tpt) outliers start: 24 outliers final: 14 residues processed: 118 average time/residue: 0.5440 time to fit residues: 68.7649 Evaluate side-chains 126 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 412 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 68 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 chunk 57 optimal weight: 20.0000 chunk 27 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 17 optimal weight: 8.9990 chunk 52 optimal weight: 9.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 GLN ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 GLN ** B 76 GLN ** 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 = 0.3643 r_free = 0.3643 target = 0.149227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.113358 restraints weight = 8158.161| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.24 r_work: 0.3030 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8490 Z= 0.177 Angle : 0.666 7.834 11588 Z= 0.324 Chirality : 0.044 0.160 1422 Planarity : 0.005 0.041 1352 Dihedral : 12.973 132.996 1940 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.62 % Allowed : 16.19 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.26), residues: 1012 helix: 1.50 (0.19), residues: 666 sheet: None (None), residues: 0 loop : 1.14 (0.37), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 456 TYR 0.013 0.002 TYR A 42 PHE 0.019 0.002 PHE A 459 TRP 0.016 0.002 TRP B 149 HIS 0.003 0.001 HIS B 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 ( 8488) covalent geometry : angle 0.66622 / 0.32 (11588) hydrogen bonds : bond 0.05639 / 4.04 ( 506) hydrogen bonds : angle 4.96778 / 3.57 ( 1452) Misc. bond : bond 0.00026 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.265 Fit side-chains REVERT: A 161 MET cc_start: 0.9059 (mtp) cc_final: 0.8635 (mtm) REVERT: A 172 LEU cc_start: 0.8545 (tp) cc_final: 0.8127 (mt) REVERT: A 251 ILE cc_start: 0.7507 (OUTLIER) cc_final: 0.7147 (pt) REVERT: A 550 MET cc_start: 0.5006 (tpt) cc_final: 0.4165 (tpt) REVERT: B 161 MET cc_start: 0.9060 (mtp) cc_final: 0.8636 (mtm) REVERT: B 172 LEU cc_start: 0.8543 (tp) cc_final: 0.8128 (mt) REVERT: B 251 ILE cc_start: 0.7505 (OUTLIER) cc_final: 0.7144 (pt) REVERT: B 550 MET cc_start: 0.5006 (tpt) cc_final: 0.4167 (tpt) outliers start: 22 outliers final: 14 residues processed: 116 average time/residue: 0.5243 time to fit residues: 65.1087 Evaluate side-chains 126 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 412 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 10.0000 chunk 77 optimal weight: 0.0020 chunk 1 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 35 optimal weight: 30.0000 chunk 9 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 93 optimal weight: 7.9990 chunk 42 optimal weight: 0.6980 chunk 13 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 overall best weight: 4.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 GLN ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 GLN ** B 76 GLN ** 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 = 0.3640 r_free = 0.3640 target = 0.148901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.114243 restraints weight = 8104.336| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.17 r_work: 0.3019 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8490 Z= 0.194 Angle : 0.691 8.051 11588 Z= 0.337 Chirality : 0.045 0.166 1422 Planarity : 0.005 0.041 1352 Dihedral : 13.204 133.135 1940 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.26 % Allowed : 16.31 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.26), residues: 1012 helix: 1.41 (0.19), residues: 664 sheet: None (None), residues: 0 loop : 1.01 (0.37), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 456 TYR 0.014 0.002 TYR B 42 PHE 0.023 0.003 PHE A 436 TRP 0.018 0.002 TRP A 149 HIS 0.003 0.001 HIS A 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.19 ( 8488) covalent geometry : angle 0.69121 / 0.34 (11588) hydrogen bonds : bond 0.05838 / 4.18 ( 506) hydrogen bonds : angle 5.04156 / 3.62 ( 1452) Misc. bond : bond 0.00030 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.389 Fit side-chains REVERT: A 161 MET cc_start: 0.9069 (mtp) cc_final: 0.8649 (mtm) REVERT: A 172 LEU cc_start: 0.8560 (tp) cc_final: 0.8140 (mt) REVERT: A 251 ILE cc_start: 0.7565 (OUTLIER) cc_final: 0.7182 (pt) REVERT: A 550 MET cc_start: 0.5034 (tpt) cc_final: 0.4183 (tpt) REVERT: B 161 MET cc_start: 0.9069 (mtp) cc_final: 0.8651 (mtm) REVERT: B 172 LEU cc_start: 0.8557 (tp) cc_final: 0.8142 (mt) REVERT: B 251 ILE cc_start: 0.7562 (OUTLIER) cc_final: 0.7178 (pt) REVERT: B 550 MET cc_start: 0.5025 (tpt) cc_final: 0.4175 (tpt) outliers start: 19 outliers final: 16 residues processed: 119 average time/residue: 0.5811 time to fit residues: 73.8540 Evaluate side-chains 130 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 489 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 2.9990 chunk 26 optimal weight: 0.0070 chunk 95 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 73 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 overall best weight: 2.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 GLN B 50 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.150860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.116410 restraints weight = 8136.364| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.17 r_work: 0.3087 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8490 Z= 0.154 Angle : 0.645 9.393 11588 Z= 0.311 Chirality : 0.043 0.152 1422 Planarity : 0.005 0.042 1352 Dihedral : 13.001 132.967 1940 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.38 % Allowed : 15.71 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.26), residues: 1012 helix: 1.52 (0.19), residues: 678 sheet: None (None), residues: 0 loop : 1.15 (0.38), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 456 TYR 0.011 0.002 TYR A 42 PHE 0.019 0.002 PHE A 436 TRP 0.016 0.002 TRP B 149 HIS 0.002 0.001 HIS B 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 ( 8488) covalent geometry : angle 0.64463 / 0.31 (11588) hydrogen bonds : bond 0.05253 / 3.76 ( 506) hydrogen bonds : angle 4.91592 / 3.52 ( 1452) Misc. bond : bond 0.00023 / 0.01 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.303 Fit side-chains REVERT: A 161 MET cc_start: 0.9028 (mtp) cc_final: 0.8611 (mtm) REVERT: A 172 LEU cc_start: 0.8515 (tp) cc_final: 0.8110 (mt) REVERT: A 251 ILE cc_start: 0.7525 (OUTLIER) cc_final: 0.7171 (pt) REVERT: A 550 MET cc_start: 0.5180 (tpt) cc_final: 0.4355 (tpt) REVERT: B 161 MET cc_start: 0.9030 (mtp) cc_final: 0.8612 (mtm) REVERT: B 172 LEU cc_start: 0.8519 (tp) cc_final: 0.8122 (mt) REVERT: B 251 ILE cc_start: 0.7522 (OUTLIER) cc_final: 0.7165 (pt) REVERT: B 438 MET cc_start: 0.8996 (OUTLIER) cc_final: 0.8771 (tpt) REVERT: B 550 MET cc_start: 0.5162 (tpt) cc_final: 0.4345 (tpt) outliers start: 20 outliers final: 15 residues processed: 118 average time/residue: 0.5458 time to fit residues: 68.9529 Evaluate side-chains 131 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 438 MET Chi-restraints excluded: chain B residue 489 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 34 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 30 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 74 optimal weight: 0.0030 chunk 11 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 28 optimal weight: 8.9990 chunk 19 optimal weight: 9.9990 overall best weight: 1.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 GLN B 50 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.153308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.119120 restraints weight = 8201.153| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.18 r_work: 0.3127 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8490 Z= 0.120 Angle : 0.592 9.157 11588 Z= 0.284 Chirality : 0.041 0.136 1422 Planarity : 0.005 0.042 1352 Dihedral : 12.633 134.544 1940 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.79 % Allowed : 16.55 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.27), residues: 1012 helix: 1.73 (0.19), residues: 676 sheet: None (None), residues: 0 loop : 1.31 (0.39), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 456 TYR 0.008 0.001 TYR A 42 PHE 0.018 0.002 PHE B 420 TRP 0.012 0.001 TRP A 149 HIS 0.002 0.000 HIS B 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 ( 8488) covalent geometry : angle 0.59239 / 0.28 (11588) hydrogen bonds : bond 0.04488 / 3.22 ( 506) hydrogen bonds : angle 4.68894 / 3.36 ( 1452) Misc. bond : bond 0.00012 / 0.01 ( 2) =============================================================================== Job complete usr+sys time: 3145.36 seconds wall clock time: 54 minutes 19.97 seconds (3259.97 seconds total)