Starting phenix.real_space_refine on Wed Mar 12 21:16:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jew_36201/03_2025/8jew_36201.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jew_36201/03_2025/8jew_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_36201/03_2025/8jew_36201.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jew_36201/03_2025/8jew_36201.map" model { file = "/net/cci-nas-00/data/ceres_data/8jew_36201/03_2025/8jew_36201.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jew_36201/03_2025/8jew_36201.cif" } resolution = 2.49 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'PHE:plan': 1, 'GLU:plan': 2} 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: {'PLM:plan-1': 1, 'LBN:plan-3': 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: 7.99, per 1000 atoms: 0.96 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: 2.62 Conformation dependent library (CDL) restraints added in 926.8 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: 0.75 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: 2.25 Time building geometry restraints manager: 2.96 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: 0.04 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.190 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 24.860 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 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:11.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 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 8488 Z= 0.973 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (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 TRP 0.058 0.012 TRP A 311 HIS 0.014 0.005 HIS A 210 PHE 0.050 0.010 PHE A 459 TYR 0.043 0.009 TYR B 474 ARG 0.021 0.003 ARG B 555 *********************** 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 : 0.917 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: 0.3350 (tpt) cc_final: 0.3060 (tpt) REVERT: B 78 MET cc_start: 0.8858 (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: 0.7762 (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: 1.1810 time to fit residues: 186.6112 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 : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 9.9990 chunk 77 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 26 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 41 optimal weight: 0.7980 chunk 79 optimal weight: 0.4980 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 ASN ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 GLN B 147 HIS B 483 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.153255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.118829 restraints weight = 7830.010| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.33 r_work: 0.3121 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.122 8488 Z= 0.388 Angle : 1.244 39.011 11588 Z= 0.572 Chirality : 0.066 0.514 1422 Planarity : 0.013 0.192 1352 Dihedral : 12.973 127.471 1940 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.99 % Allowed : 2.27 % Favored : 96.74 % Rotamer: Outliers : 4.29 % Allowed : 13.69 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.26), residues: 1012 helix: 0.19 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -0.89 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.004 TRP B 265 HIS 0.059 0.007 HIS B 210 PHE 0.101 0.006 PHE B 255 TYR 0.181 0.008 TYR B 402 ARG 0.068 0.005 ARG B 456 *********************** 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 175 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 139 time to evaluate : 0.913 Fit side-chains REVERT: A 78 MET cc_start: 0.8763 (tmt) cc_final: 0.8311 (tmt) REVERT: A 161 MET cc_start: 0.9002 (mtp) cc_final: 0.8574 (mtm) REVERT: A 172 LEU cc_start: 0.8619 (tp) cc_final: 0.8198 (mt) REVERT: A 251 ILE cc_start: 0.7602 (tt) cc_final: 0.7220 (pt) REVERT: A 550 MET cc_start: 0.4903 (tpt) cc_final: 0.4424 (tpt) REVERT: B 78 MET cc_start: 0.8681 (tmt) cc_final: 0.8207 (tmt) REVERT: B 172 LEU cc_start: 0.8531 (tp) cc_final: 0.8114 (OUTLIER) REVERT: B 249 ILE cc_start: 0.5805 (OUTLIER) cc_final: 0.5026 (mm) REVERT: B 251 ILE cc_start: 0.7768 (OUTLIER) cc_final: 0.7259 (pt) REVERT: B 282 LYS cc_start: 0.7976 (mtmm) cc_final: 0.7545 (mtpm) REVERT: B 550 MET cc_start: 0.4963 (tpt) cc_final: 0.4506 (tpt) outliers start: 36 outliers final: 8 residues processed: 160 average time/residue: 1.0069 time to fit residues: 173.2260 Evaluate side-chains 128 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 412 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 89 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 chunk 62 optimal weight: 0.2980 chunk 98 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 100 optimal weight: 20.0000 chunk 95 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 97 optimal weight: 0.9990 chunk 7 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 GLN B 108 GLN B 473 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.150152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.112804 restraints weight = 7926.878| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.26 r_work: 0.3051 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8488 Z= 0.223 Angle : 0.668 8.765 11588 Z= 0.324 Chirality : 0.043 0.179 1422 Planarity : 0.005 0.045 1352 Dihedral : 12.643 130.821 1940 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.55 % Allowed : 16.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.26), residues: 1012 helix: 1.21 (0.19), residues: 664 sheet: None (None), residues: 0 loop : 0.11 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 149 HIS 0.004 0.001 HIS B 354 PHE 0.021 0.002 PHE B 502 TYR 0.016 0.002 TYR B 339 ARG 0.006 0.001 ARG B 456 *********************** 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 137 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.822 Fit side-chains REVERT: A 78 MET cc_start: 0.8788 (tmt) cc_final: 0.8379 (tmt) REVERT: A 161 MET cc_start: 0.9025 (mtp) cc_final: 0.8595 (mtm) REVERT: A 172 LEU cc_start: 0.8510 (tp) cc_final: 0.8137 (mt) REVERT: A 251 ILE cc_start: 0.7693 (OUTLIER) cc_final: 0.7244 (pt) REVERT: A 550 MET cc_start: 0.4872 (tpt) cc_final: 0.4375 (tpt) REVERT: B 172 LEU cc_start: 0.8557 (tp) cc_final: 0.8034 (mt) REVERT: B 251 ILE cc_start: 0.7675 (tt) cc_final: 0.7337 (pt) REVERT: B 282 LYS cc_start: 0.7921 (mtmm) cc_final: 0.7469 (mtpm) REVERT: B 476 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7488 (pt0) REVERT: B 483 ASN cc_start: 0.7685 (t0) cc_final: 0.7479 (t0) REVERT: B 550 MET cc_start: 0.4965 (tpt) cc_final: 0.4493 (tpt) outliers start: 13 outliers final: 5 residues processed: 129 average time/residue: 1.1204 time to fit residues: 154.5605 Evaluate side-chains 119 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 112 time to evaluate : 0.816 ------------------------------------------------------------------------------- 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 313 LEU Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 476 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 38 optimal weight: 6.9990 chunk 54 optimal weight: 0.6980 chunk 96 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 57 optimal weight: 9.9990 chunk 43 optimal weight: 9.9990 chunk 76 optimal weight: 20.0000 chunk 70 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.150903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.116197 restraints weight = 8090.519| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.16 r_work: 0.3105 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8488 Z= 0.222 Angle : 0.637 7.816 11588 Z= 0.309 Chirality : 0.043 0.145 1422 Planarity : 0.006 0.050 1352 Dihedral : 12.636 133.481 1940 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.50 % Allowed : 15.36 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.26), residues: 1012 helix: 1.42 (0.19), residues: 678 sheet: None (None), residues: 0 loop : 0.81 (0.37), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 149 HIS 0.002 0.001 HIS B 51 PHE 0.018 0.002 PHE B 502 TYR 0.009 0.001 TYR A 42 ARG 0.005 0.001 ARG B 456 *********************** 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 141 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.933 Fit side-chains REVERT: A 161 MET cc_start: 0.9014 (mtp) cc_final: 0.8591 (mtm) REVERT: A 172 LEU cc_start: 0.8473 (tp) cc_final: 0.8095 (mt) REVERT: A 251 ILE cc_start: 0.7683 (OUTLIER) cc_final: 0.7232 (pt) REVERT: A 550 MET cc_start: 0.5017 (tpt) cc_final: 0.4539 (tpt) REVERT: B 116 VAL cc_start: 0.8581 (t) cc_final: 0.8363 (t) REVERT: B 172 LEU cc_start: 0.8617 (tp) cc_final: 0.8133 (mt) REVERT: B 251 ILE cc_start: 0.7703 (OUTLIER) cc_final: 0.7304 (pt) REVERT: B 254 MET cc_start: 0.7338 (mtp) cc_final: 0.7103 (mtm) REVERT: B 282 LYS cc_start: 0.7857 (mtmm) cc_final: 0.7452 (mtpm) REVERT: B 483 ASN cc_start: 0.7893 (t0) cc_final: 0.7669 (t0) REVERT: B 550 MET cc_start: 0.5053 (tpt) cc_final: 0.4376 (tpt) outliers start: 21 outliers final: 12 residues processed: 126 average time/residue: 1.1582 time to fit residues: 156.2308 Evaluate side-chains 128 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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 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 119 LYS 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 97 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 6 optimal weight: 20.0000 chunk 88 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 57 optimal weight: 20.0000 chunk 45 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.151693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.116818 restraints weight = 8058.243| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.18 r_work: 0.3095 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8488 Z= 0.205 Angle : 0.625 8.755 11588 Z= 0.299 Chirality : 0.042 0.138 1422 Planarity : 0.005 0.052 1352 Dihedral : 12.482 134.859 1940 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.13 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.27), residues: 1012 helix: 1.59 (0.19), residues: 678 sheet: None (None), residues: 0 loop : 1.10 (0.38), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 149 HIS 0.002 0.001 HIS B 51 PHE 0.016 0.002 PHE B 459 TYR 0.009 0.001 TYR A 42 ARG 0.005 0.000 ARG B 456 *********************** 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 144 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.908 Fit side-chains REVERT: A 78 MET cc_start: 0.8785 (tmt) cc_final: 0.8365 (tmt) REVERT: A 161 MET cc_start: 0.9015 (mtp) cc_final: 0.8596 (mtm) REVERT: A 172 LEU cc_start: 0.8439 (tp) cc_final: 0.8073 (mt) REVERT: A 251 ILE cc_start: 0.7676 (OUTLIER) cc_final: 0.7301 (pt) REVERT: A 550 MET cc_start: 0.5236 (tpt) cc_final: 0.4464 (tpt) REVERT: B 172 LEU cc_start: 0.8501 (tp) cc_final: 0.8083 (mt) REVERT: B 251 ILE cc_start: 0.7728 (OUTLIER) cc_final: 0.7335 (pt) REVERT: B 254 MET cc_start: 0.7335 (mtp) cc_final: 0.7105 (mtm) REVERT: B 282 LYS cc_start: 0.7831 (mtmm) cc_final: 0.7419 (mtpm) REVERT: B 483 ASN cc_start: 0.7877 (t0) cc_final: 0.7668 (t160) REVERT: B 550 MET cc_start: 0.5181 (tpt) cc_final: 0.4474 (tpt) outliers start: 24 outliers final: 9 residues processed: 132 average time/residue: 1.0814 time to fit residues: 153.0315 Evaluate side-chains 118 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.875 ------------------------------------------------------------------------------- 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 407 MET Chi-restraints excluded: chain B residue 119 LYS 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 407 MET Chi-restraints excluded: chain B residue 412 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 63 optimal weight: 9.9990 chunk 26 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 31 optimal weight: 20.0000 chunk 20 optimal weight: 8.9990 chunk 47 optimal weight: 0.3980 chunk 101 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 GLN B 76 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.151441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.116640 restraints weight = 8121.954| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.18 r_work: 0.3094 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8488 Z= 0.207 Angle : 0.628 7.643 11588 Z= 0.300 Chirality : 0.042 0.139 1422 Planarity : 0.005 0.050 1352 Dihedral : 12.373 135.284 1940 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.10 % Allowed : 16.31 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.27), residues: 1012 helix: 1.64 (0.19), residues: 678 sheet: None (None), residues: 0 loop : 1.23 (0.38), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 149 HIS 0.002 0.001 HIS A 354 PHE 0.016 0.002 PHE A 459 TYR 0.010 0.001 TYR A 42 ARG 0.004 0.000 ARG B 456 *********************** 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 142 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 0.845 Fit side-chains REVERT: A 161 MET cc_start: 0.9009 (mtp) cc_final: 0.8593 (mtm) REVERT: A 172 LEU cc_start: 0.8453 (tp) cc_final: 0.8062 (mt) REVERT: A 251 ILE cc_start: 0.7623 (OUTLIER) cc_final: 0.7251 (pt) REVERT: A 550 MET cc_start: 0.5108 (tpt) cc_final: 0.4276 (tpt) REVERT: B 172 LEU cc_start: 0.8457 (tp) cc_final: 0.8061 (mt) REVERT: B 251 ILE cc_start: 0.7719 (OUTLIER) cc_final: 0.7348 (pt) REVERT: B 282 LYS cc_start: 0.7891 (mtmm) cc_final: 0.7486 (mtpm) REVERT: B 483 ASN cc_start: 0.7917 (t0) cc_final: 0.7707 (t160) REVERT: B 550 MET cc_start: 0.5066 (tpt) cc_final: 0.4255 (tpt) outliers start: 26 outliers final: 13 residues processed: 127 average time/residue: 1.3028 time to fit residues: 177.4541 Evaluate side-chains 124 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 1.068 ------------------------------------------------------------------------------- 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 119 LYS 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 76 optimal weight: 20.0000 chunk 27 optimal weight: 0.8980 chunk 29 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 23 optimal weight: 0.0570 overall best weight: 2.5904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.150975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.116263 restraints weight = 8115.192| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.17 r_work: 0.3056 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8488 Z= 0.227 Angle : 0.644 7.728 11588 Z= 0.309 Chirality : 0.043 0.143 1422 Planarity : 0.005 0.049 1352 Dihedral : 12.376 135.043 1940 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.74 % Allowed : 17.02 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.26), residues: 1012 helix: 1.61 (0.19), residues: 678 sheet: None (None), residues: 0 loop : 1.28 (0.38), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 149 HIS 0.002 0.001 HIS A 354 PHE 0.017 0.002 PHE A 459 TYR 0.011 0.001 TYR A 42 ARG 0.005 0.000 ARG B 456 *********************** 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 138 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.993 Fit side-chains REVERT: A 161 MET cc_start: 0.9010 (mtp) cc_final: 0.8583 (mtm) REVERT: A 172 LEU cc_start: 0.8472 (tp) cc_final: 0.8085 (mt) REVERT: A 251 ILE cc_start: 0.7594 (OUTLIER) cc_final: 0.7233 (pt) REVERT: A 550 MET cc_start: 0.5078 (tpt) cc_final: 0.4200 (tpt) REVERT: B 172 LEU cc_start: 0.8499 (tp) cc_final: 0.8098 (mt) REVERT: B 251 ILE cc_start: 0.7686 (OUTLIER) cc_final: 0.7324 (pt) REVERT: B 282 LYS cc_start: 0.7902 (mtmm) cc_final: 0.7498 (mtpm) REVERT: B 476 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7653 (mp0) REVERT: B 483 ASN cc_start: 0.7896 (t0) cc_final: 0.7690 (t160) outliers start: 23 outliers final: 14 residues processed: 124 average time/residue: 1.1938 time to fit residues: 159.1491 Evaluate side-chains 130 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.857 ------------------------------------------------------------------------------- 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 119 LYS 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 Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 476 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 40 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 20 optimal weight: 0.0970 chunk 1 optimal weight: 10.0000 chunk 59 optimal weight: 0.6980 chunk 72 optimal weight: 8.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3654 r_free = 0.3654 target = 0.150643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.113586 restraints weight = 7980.140| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.28 r_work: 0.3098 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8488 Z= 0.188 Angle : 0.614 7.430 11588 Z= 0.293 Chirality : 0.041 0.134 1422 Planarity : 0.005 0.047 1352 Dihedral : 12.129 135.307 1940 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.38 % Allowed : 17.86 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.27), residues: 1012 helix: 1.74 (0.19), residues: 678 sheet: None (None), residues: 0 loop : 1.34 (0.38), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 149 HIS 0.002 0.001 HIS A 354 PHE 0.015 0.002 PHE A 420 TYR 0.009 0.001 TYR A 42 ARG 0.003 0.000 ARG B 456 *********************** 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 136 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.826 Fit side-chains REVERT: A 161 MET cc_start: 0.9016 (mtp) cc_final: 0.8604 (mtm) REVERT: A 172 LEU cc_start: 0.8448 (tp) cc_final: 0.8051 (mt) REVERT: A 251 ILE cc_start: 0.7511 (OUTLIER) cc_final: 0.7174 (pt) REVERT: A 550 MET cc_start: 0.4973 (tpt) cc_final: 0.4064 (tpt) REVERT: B 172 LEU cc_start: 0.8431 (tp) cc_final: 0.8057 (mt) REVERT: B 251 ILE cc_start: 0.7654 (OUTLIER) cc_final: 0.7360 (pt) REVERT: B 282 LYS cc_start: 0.7920 (mtmm) cc_final: 0.7493 (mtpm) REVERT: B 452 MET cc_start: 0.8482 (mmp) cc_final: 0.8271 (mmm) REVERT: B 483 ASN cc_start: 0.7879 (t0) cc_final: 0.7677 (t160) outliers start: 20 outliers final: 14 residues processed: 124 average time/residue: 1.0876 time to fit residues: 144.3514 Evaluate side-chains 130 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.817 ------------------------------------------------------------------------------- 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 119 LYS Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 296 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 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 86 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 483 ASN B 50 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.148433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.111440 restraints weight = 8016.915| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.26 r_work: 0.3020 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8488 Z= 0.285 Angle : 0.689 7.925 11588 Z= 0.332 Chirality : 0.045 0.161 1422 Planarity : 0.006 0.046 1352 Dihedral : 12.487 134.023 1940 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.26 % Allowed : 17.74 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.26), residues: 1012 helix: 1.54 (0.19), residues: 666 sheet: None (None), residues: 0 loop : 1.21 (0.38), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 149 HIS 0.003 0.001 HIS B 51 PHE 0.020 0.003 PHE B 200 TYR 0.014 0.002 TYR A 42 ARG 0.007 0.001 ARG B 456 *********************** 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 134 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 1.005 Fit side-chains REVERT: A 161 MET cc_start: 0.9045 (mtp) cc_final: 0.8669 (mtm) REVERT: A 172 LEU cc_start: 0.8550 (tp) cc_final: 0.8120 (mt) REVERT: A 251 ILE cc_start: 0.7558 (OUTLIER) cc_final: 0.7208 (pt) REVERT: A 550 MET cc_start: 0.4899 (tpt) cc_final: 0.3993 (tpt) REVERT: B 172 LEU cc_start: 0.8511 (tp) cc_final: 0.8095 (mt) REVERT: B 251 ILE cc_start: 0.7623 (OUTLIER) cc_final: 0.7312 (pt) REVERT: B 282 LYS cc_start: 0.7906 (mtmm) cc_final: 0.7473 (mtpm) outliers start: 19 outliers final: 14 residues processed: 123 average time/residue: 1.1686 time to fit residues: 153.6083 Evaluate side-chains 131 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.849 ------------------------------------------------------------------------------- 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 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 119 LYS Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 296 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 Chi-restraints excluded: chain B residue 412 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 55 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN B 50 GLN B 483 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.151412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.114595 restraints weight = 7972.206| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.27 r_work: 0.3100 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8488 Z= 0.161 Angle : 0.608 9.604 11588 Z= 0.287 Chirality : 0.041 0.138 1422 Planarity : 0.005 0.046 1352 Dihedral : 11.958 135.145 1940 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.02 % Allowed : 18.10 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.27), residues: 1012 helix: 1.80 (0.19), residues: 678 sheet: None (None), residues: 0 loop : 1.37 (0.39), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 149 HIS 0.002 0.000 HIS A 354 PHE 0.017 0.002 PHE A 420 TYR 0.008 0.001 TYR A 42 ARG 0.001 0.000 ARG A 126 ********************** 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 130 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 1.919 Fit side-chains REVERT: A 161 MET cc_start: 0.9014 (mtp) cc_final: 0.8608 (mtm) REVERT: A 172 LEU cc_start: 0.8464 (tp) cc_final: 0.8043 (mt) REVERT: A 251 ILE cc_start: 0.7543 (OUTLIER) cc_final: 0.7236 (pt) REVERT: B 172 LEU cc_start: 0.8392 (tp) cc_final: 0.8020 (mt) REVERT: B 251 ILE cc_start: 0.7676 (OUTLIER) cc_final: 0.7413 (pt) REVERT: B 452 MET cc_start: 0.8491 (mmp) cc_final: 0.8237 (mmm) outliers start: 17 outliers final: 12 residues processed: 119 average time/residue: 1.7810 time to fit residues: 227.7398 Evaluate side-chains 124 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 1.118 ------------------------------------------------------------------------------- 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 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 B residue 102 ILE Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 296 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 Chi-restraints excluded: chain B residue 412 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 74 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 77 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.150619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.114922 restraints weight = 8257.789| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.25 r_work: 0.3082 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8488 Z= 0.225 Angle : 0.654 9.404 11588 Z= 0.312 Chirality : 0.043 0.142 1422 Planarity : 0.005 0.045 1352 Dihedral : 12.139 134.829 1940 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.90 % Allowed : 18.10 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.27), residues: 1012 helix: 1.64 (0.19), residues: 678 sheet: None (None), residues: 0 loop : 1.31 (0.38), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 149 HIS 0.002 0.001 HIS A 354 PHE 0.020 0.002 PHE A 420 TYR 0.011 0.001 TYR A 42 ARG 0.004 0.000 ARG B 456 =============================================================================== Job complete usr+sys time: 6959.39 seconds wall clock time: 122 minutes 34.36 seconds (7354.36 seconds total)