Starting phenix.real_space_refine on Sun May 11 18:30:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jew_36201/05_2025/8jew_36201.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jew_36201/05_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_36201/05_2025/8jew_36201.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jew_36201/05_2025/8jew_36201.map" model { file = "/net/cci-nas-00/data/ceres_data/8jew_36201/05_2025/8jew_36201.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jew_36201/05_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 7.98, 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: 2.58 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.73 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: 2.33 Time building geometry restraints manager: 2.89 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: 0.100 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.010 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.280 ------------------------------------------------------------------------------- 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 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.18082 ( 506) hydrogen bonds : angle 7.15593 ( 1452) covalent geometry : bond 0.01479 ( 8488) covalent geometry : angle 1.79076 (11588) Misc. bond : bond 0.01839 ( 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 : 0.892 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: 1.1169 time to fit residues: 177.1175 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 : 0.965 ------------------------------------------------------------------------------- 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 = 0.153265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.118862 restraints weight = 7829.823| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.33 r_work: 0.3118 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.116 8490 Z= 0.235 Angle : 1.243 39.130 11588 Z= 0.572 Chirality : 0.066 0.513 1422 Planarity : 0.013 0.192 1352 Dihedral : 12.970 127.441 1940 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.61 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 0.058 0.007 HIS B 210 PHE 0.100 0.006 PHE B 255 TYR 0.181 0.008 TYR B 402 ARG 0.067 0.005 ARG B 456 Details of bonding type rmsd hydrogen bonds : bond 0.06595 ( 506) hydrogen bonds : angle 5.62549 ( 1452) covalent geometry : bond 0.00549 ( 8488) covalent geometry : angle 1.24299 (11588) Misc. bond : bond 0.00016 ( 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 174 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 138 time to evaluate : 0.905 Fit side-chains REVERT: A 78 MET cc_start: 0.8766 (tmt) cc_final: 0.8312 (tmt) REVERT: A 161 MET cc_start: 0.8999 (mtp) cc_final: 0.8573 (mtm) REVERT: A 172 LEU cc_start: 0.8619 (tp) cc_final: 0.8195 (mt) REVERT: A 251 ILE cc_start: 0.7604 (tt) cc_final: 0.7222 (pt) REVERT: A 550 MET cc_start: 0.4928 (tpt) cc_final: 0.4448 (tpt) REVERT: B 78 MET cc_start: 0.8684 (tmt) cc_final: 0.8208 (tmt) REVERT: B 172 LEU cc_start: 0.8529 (tp) cc_final: 0.8114 (OUTLIER) REVERT: B 249 ILE cc_start: 0.5808 (OUTLIER) cc_final: 0.5032 (mm) REVERT: B 251 ILE cc_start: 0.7767 (OUTLIER) cc_final: 0.7260 (pt) REVERT: B 282 LYS cc_start: 0.7979 (mtmm) cc_final: 0.7546 (mtpm) REVERT: B 550 MET cc_start: 0.4992 (tpt) cc_final: 0.4533 (tpt) outliers start: 36 outliers final: 8 residues processed: 159 average time/residue: 1.0354 time to fit residues: 176.8142 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 : 0.858 ------------------------------------------------------------------------------- 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: 7.9990 chunk 62 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 100 optimal weight: 0.0770 chunk 95 optimal weight: 0.8980 chunk 22 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.9944 ------------------------------------------------------------------------------- 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 = 0.3660 r_free = 0.3660 target = 0.150374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.113172 restraints weight = 7940.872| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.26 r_work: 0.3053 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8490 Z= 0.146 Angle : 0.656 8.558 11588 Z= 0.318 Chirality : 0.043 0.171 1422 Planarity : 0.005 0.046 1352 Dihedral : 12.583 131.537 1940 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.90 % Allowed : 15.95 % 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: 1.20 (0.26), residues: 1012 helix: 1.18 (0.19), residues: 678 sheet: None (None), residues: 0 loop : 0.18 (0.36), residues: 334 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 0.017 0.002 TYR B 339 ARG 0.007 0.001 ARG B 456 Details of bonding type rmsd hydrogen bonds : bond 0.05241 ( 506) hydrogen bonds : angle 4.96149 ( 1452) covalent geometry : bond 0.00320 ( 8488) covalent geometry : angle 0.65554 (11588) Misc. bond : bond 0.00018 ( 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 136 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.955 Fit side-chains REVERT: A 161 MET cc_start: 0.9021 (mtp) cc_final: 0.8644 (mtm) REVERT: A 172 LEU cc_start: 0.8486 (tp) cc_final: 0.8119 (mt) REVERT: A 251 ILE cc_start: 0.7626 (OUTLIER) cc_final: 0.7175 (pt) REVERT: A 550 MET cc_start: 0.4875 (tpt) cc_final: 0.4374 (tpt) REVERT: B 172 LEU cc_start: 0.8551 (tp) cc_final: 0.8024 (mt) REVERT: B 251 ILE cc_start: 0.7709 (OUTLIER) cc_final: 0.7375 (pt) REVERT: B 282 LYS cc_start: 0.7936 (mtmm) cc_final: 0.7479 (mtpm) REVERT: B 476 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7503 (pt0) REVERT: B 550 MET cc_start: 0.4991 (tpt) cc_final: 0.4520 (tpt) outliers start: 16 outliers final: 5 residues processed: 128 average time/residue: 1.0936 time to fit residues: 150.3607 Evaluate side-chains 119 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 0.867 ------------------------------------------------------------------------------- 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 B residue 251 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 38 optimal weight: 6.9990 chunk 54 optimal weight: 0.7980 chunk 96 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 76 optimal weight: 20.0000 chunk 70 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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 483 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.149064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.112027 restraints weight = 7853.710| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.25 r_work: 0.3041 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8490 Z= 0.169 Angle : 0.666 8.041 11588 Z= 0.323 Chirality : 0.044 0.153 1422 Planarity : 0.006 0.049 1352 Dihedral : 12.770 133.239 1940 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.26 % Allowed : 15.71 % Favored : 82.02 % 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: 1.68 (0.26), residues: 1012 helix: 1.41 (0.19), residues: 664 sheet: None (None), residues: 0 loop : 0.76 (0.37), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 149 HIS 0.003 0.001 HIS A 354 PHE 0.019 0.002 PHE B 502 TYR 0.011 0.002 TYR B 474 ARG 0.008 0.001 ARG B 456 Details of bonding type rmsd hydrogen bonds : bond 0.05596 ( 506) hydrogen bonds : angle 4.98670 ( 1452) covalent geometry : bond 0.00383 ( 8488) covalent geometry : angle 0.66584 (11588) Misc. bond : bond 0.00020 ( 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 133 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.852 Fit side-chains REVERT: A 161 MET cc_start: 0.9024 (mtp) cc_final: 0.8588 (mtm) REVERT: A 172 LEU cc_start: 0.8496 (tp) cc_final: 0.8109 (mt) REVERT: A 251 ILE cc_start: 0.7687 (OUTLIER) cc_final: 0.7229 (pt) REVERT: A 550 MET cc_start: 0.4891 (tpt) cc_final: 0.4414 (tpt) REVERT: B 172 LEU cc_start: 0.8634 (tp) cc_final: 0.8136 (mt) REVERT: B 251 ILE cc_start: 0.7733 (OUTLIER) cc_final: 0.7314 (pt) REVERT: B 282 LYS cc_start: 0.7846 (mtmm) cc_final: 0.7402 (mtpm) REVERT: B 550 MET cc_start: 0.4965 (tpt) cc_final: 0.4284 (tpt) outliers start: 19 outliers final: 12 residues processed: 118 average time/residue: 1.1677 time to fit residues: 147.3864 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 : 0.896 ------------------------------------------------------------------------------- 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: 6.9990 chunk 66 optimal weight: 3.9990 chunk 6 optimal weight: 20.0000 chunk 88 optimal weight: 8.9990 chunk 80 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 = 0.3607 r_free = 0.3607 target = 0.146296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.109257 restraints weight = 7850.176| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.24 r_work: 0.3004 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 8490 Z= 0.272 Angle : 0.811 8.607 11588 Z= 0.393 Chirality : 0.050 0.196 1422 Planarity : 0.007 0.050 1352 Dihedral : 13.836 134.302 1940 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.38 % Allowed : 16.31 % Favored : 81.31 % 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: 1.21 (0.26), residues: 1012 helix: 1.03 (0.19), residues: 664 sheet: None (None), residues: 0 loop : 0.61 (0.37), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 149 HIS 0.005 0.001 HIS B 51 PHE 0.027 0.003 PHE A 200 TYR 0.018 0.002 TYR A 42 ARG 0.010 0.001 ARG B 456 Details of bonding type rmsd hydrogen bonds : bond 0.06778 ( 506) hydrogen bonds : angle 5.27732 ( 1452) covalent geometry : bond 0.00650 ( 8488) covalent geometry : angle 0.81114 (11588) Misc. bond : bond 0.00069 ( 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 139 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.852 Fit side-chains REVERT: A 161 MET cc_start: 0.9067 (mtp) cc_final: 0.8672 (mtm) REVERT: A 172 LEU cc_start: 0.8582 (tp) cc_final: 0.8169 (mt) REVERT: A 550 MET cc_start: 0.5015 (tpt) cc_final: 0.4215 (tpt) REVERT: B 172 LEU cc_start: 0.8590 (tp) cc_final: 0.8170 (mt) REVERT: B 251 ILE cc_start: 0.7707 (OUTLIER) cc_final: 0.7228 (pt) REVERT: B 282 LYS cc_start: 0.7644 (mtmm) cc_final: 0.7194 (mtpm) REVERT: B 550 MET cc_start: 0.4988 (tpt) cc_final: 0.4177 (tpt) outliers start: 20 outliers final: 11 residues processed: 129 average time/residue: 1.0475 time to fit residues: 145.0983 Evaluate side-chains 127 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.928 ------------------------------------------------------------------------------- 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 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 344 ARG Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 476 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 63 optimal weight: 8.9990 chunk 26 optimal weight: 0.0010 chunk 80 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 101 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 overall best weight: 1.9992 ------------------------------------------------------------------------------- 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 = 0.3640 r_free = 0.3640 target = 0.149207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.112132 restraints weight = 7915.381| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.27 r_work: 0.3083 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8490 Z= 0.142 Angle : 0.631 8.024 11588 Z= 0.304 Chirality : 0.042 0.147 1422 Planarity : 0.005 0.048 1352 Dihedral : 13.119 134.373 1940 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.86 % Allowed : 15.83 % Favored : 81.31 % 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: 1.85 (0.26), residues: 1012 helix: 1.45 (0.19), residues: 678 sheet: None (None), residues: 0 loop : 1.00 (0.38), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 149 HIS 0.002 0.001 HIS A 354 PHE 0.016 0.002 PHE A 459 TYR 0.009 0.001 TYR A 474 ARG 0.003 0.000 ARG B 456 Details of bonding type rmsd hydrogen bonds : bond 0.05083 ( 506) hydrogen bonds : angle 4.93170 ( 1452) covalent geometry : bond 0.00311 ( 8488) covalent geometry : angle 0.63142 (11588) Misc. bond : bond 0.00026 ( 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 143 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.898 Fit side-chains REVERT: A 161 MET cc_start: 0.9031 (mtp) cc_final: 0.8607 (mtm) REVERT: A 172 LEU cc_start: 0.8470 (tp) cc_final: 0.8100 (mt) REVERT: A 251 ILE cc_start: 0.7586 (OUTLIER) cc_final: 0.7177 (pt) REVERT: A 550 MET cc_start: 0.5052 (tpt) cc_final: 0.4225 (tpt) REVERT: B 172 LEU cc_start: 0.8499 (tp) cc_final: 0.8074 (mt) REVERT: B 251 ILE cc_start: 0.7768 (OUTLIER) cc_final: 0.7375 (pt) REVERT: B 282 LYS cc_start: 0.7844 (mtmm) cc_final: 0.7407 (mtpm) outliers start: 24 outliers final: 10 residues processed: 129 average time/residue: 1.0483 time to fit residues: 145.1741 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 : 0.915 ------------------------------------------------------------------------------- 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 412 THR 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 255 PHE Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 344 ARG Chi-restraints excluded: chain B residue 388 VAL 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: 0.9990 chunk 29 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 10 optimal weight: 0.1980 chunk 11 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 99 optimal weight: 9.9990 chunk 78 optimal weight: 5.9990 chunk 23 optimal weight: 0.2980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 B 76 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.151583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.115074 restraints weight = 7932.304| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.25 r_work: 0.3080 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8490 Z= 0.125 Angle : 0.598 7.531 11588 Z= 0.287 Chirality : 0.041 0.135 1422 Planarity : 0.005 0.046 1352 Dihedral : 12.711 135.586 1940 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % 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: 2.22 (0.27), residues: 1012 helix: 1.72 (0.19), residues: 678 sheet: None (None), residues: 0 loop : 1.20 (0.39), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 149 HIS 0.002 0.001 HIS A 354 PHE 0.016 0.002 PHE B 361 TYR 0.008 0.001 TYR A 42 ARG 0.002 0.000 ARG B 456 Details of bonding type rmsd hydrogen bonds : bond 0.04606 ( 506) hydrogen bonds : angle 4.73141 ( 1452) covalent geometry : bond 0.00269 ( 8488) covalent geometry : angle 0.59782 (11588) Misc. bond : bond 0.00013 ( 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 140 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.972 Fit side-chains REVERT: A 161 MET cc_start: 0.9013 (mtp) cc_final: 0.8587 (mtm) REVERT: A 172 LEU cc_start: 0.8372 (tp) cc_final: 0.8027 (mt) REVERT: A 251 ILE cc_start: 0.7569 (OUTLIER) cc_final: 0.7205 (pt) REVERT: A 520 GLU cc_start: 0.7610 (mp0) cc_final: 0.7312 (mp0) REVERT: A 550 MET cc_start: 0.4957 (tpt) cc_final: 0.4065 (tpt) REVERT: B 172 LEU cc_start: 0.8461 (tp) cc_final: 0.8063 (mt) REVERT: B 251 ILE cc_start: 0.7749 (OUTLIER) cc_final: 0.7402 (pt) REVERT: B 282 LYS cc_start: 0.7933 (mtmm) cc_final: 0.7483 (mtpm) outliers start: 26 outliers final: 14 residues processed: 123 average time/residue: 1.1592 time to fit residues: 152.4854 Evaluate side-chains 124 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.865 ------------------------------------------------------------------------------- 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 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 297 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 40 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 54 optimal weight: 0.4980 chunk 10 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 59 optimal weight: 0.7980 chunk 72 optimal weight: 9.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN B 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.151879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.114981 restraints weight = 7995.196| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.27 r_work: 0.3081 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8490 Z= 0.122 Angle : 0.594 7.579 11588 Z= 0.285 Chirality : 0.041 0.135 1422 Planarity : 0.005 0.045 1352 Dihedral : 12.513 136.714 1940 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.50 % Allowed : 16.67 % Favored : 80.83 % 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: 2.39 (0.27), residues: 1012 helix: 1.82 (0.19), residues: 678 sheet: None (None), residues: 0 loop : 1.35 (0.39), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 149 HIS 0.002 0.000 HIS A 354 PHE 0.016 0.002 PHE B 361 TYR 0.008 0.001 TYR A 42 ARG 0.002 0.000 ARG B 456 Details of bonding type rmsd hydrogen bonds : bond 0.04505 ( 506) hydrogen bonds : angle 4.65664 ( 1452) covalent geometry : bond 0.00264 ( 8488) covalent geometry : angle 0.59390 (11588) Misc. bond : bond 0.00011 ( 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 134 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.838 Fit side-chains REVERT: A 161 MET cc_start: 0.9018 (mtp) cc_final: 0.8603 (mtm) REVERT: A 172 LEU cc_start: 0.8364 (tp) cc_final: 0.7994 (mt) REVERT: A 251 ILE cc_start: 0.7521 (OUTLIER) cc_final: 0.7188 (pt) REVERT: A 550 MET cc_start: 0.4932 (tpt) cc_final: 0.4068 (tpt) REVERT: B 74 HIS cc_start: 0.7918 (m-70) cc_final: 0.7700 (m-70) REVERT: B 172 LEU cc_start: 0.8416 (tp) cc_final: 0.8041 (mt) REVERT: B 251 ILE cc_start: 0.7739 (OUTLIER) cc_final: 0.7406 (pt) outliers start: 21 outliers final: 13 residues processed: 119 average time/residue: 1.1049 time to fit residues: 140.9094 Evaluate side-chains 125 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.958 ------------------------------------------------------------------------------- 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 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 313 LEU Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 407 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 90 optimal weight: 4.9990 chunk 96 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.148509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.111422 restraints weight = 8003.484| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.26 r_work: 0.3022 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8490 Z= 0.204 Angle : 0.701 8.109 11588 Z= 0.341 Chirality : 0.046 0.166 1422 Planarity : 0.006 0.045 1352 Dihedral : 12.998 134.527 1940 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.90 % Allowed : 17.38 % Favored : 80.71 % 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: 1.94 (0.26), residues: 1012 helix: 1.47 (0.19), residues: 666 sheet: None (None), residues: 0 loop : 1.19 (0.38), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 149 HIS 0.003 0.001 HIS A 354 PHE 0.023 0.003 PHE A 200 TYR 0.014 0.002 TYR A 42 ARG 0.009 0.001 ARG B 456 Details of bonding type rmsd hydrogen bonds : bond 0.05828 ( 506) hydrogen bonds : angle 4.99410 ( 1452) covalent geometry : bond 0.00484 ( 8488) covalent geometry : angle 0.70093 (11588) Misc. bond : bond 0.00026 ( 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 127 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.929 Fit side-chains REVERT: A 161 MET cc_start: 0.9068 (mtp) cc_final: 0.8692 (mtm) REVERT: A 172 LEU cc_start: 0.8502 (tp) cc_final: 0.8094 (mt) REVERT: A 251 ILE cc_start: 0.7522 (OUTLIER) cc_final: 0.7150 (pt) REVERT: A 550 MET cc_start: 0.4893 (tpt) cc_final: 0.3984 (tpt) REVERT: B 172 LEU cc_start: 0.8523 (tp) cc_final: 0.8080 (mt) REVERT: B 251 ILE cc_start: 0.7707 (OUTLIER) cc_final: 0.7333 (pt) outliers start: 16 outliers final: 10 residues processed: 116 average time/residue: 1.0744 time to fit residues: 133.8840 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 : 0.958 ------------------------------------------------------------------------------- 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 B residue 119 LYS 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 412 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 55 optimal weight: 6.9990 chunk 100 optimal weight: 8.9990 chunk 70 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 9 optimal weight: 0.1980 chunk 60 optimal weight: 6.9990 chunk 91 optimal weight: 0.2980 chunk 89 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3692 r_free = 0.3692 target = 0.153299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.118757 restraints weight = 8147.013| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.19 r_work: 0.3099 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 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 8490 Z= 0.119 Angle : 0.591 8.150 11588 Z= 0.283 Chirality : 0.041 0.138 1422 Planarity : 0.005 0.045 1352 Dihedral : 12.292 135.585 1940 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.43 % Allowed : 17.62 % Favored : 80.95 % 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: 2.36 (0.27), residues: 1012 helix: 1.77 (0.19), residues: 678 sheet: None (None), residues: 0 loop : 1.41 (0.39), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 149 HIS 0.002 0.000 HIS B 150 PHE 0.017 0.002 PHE A 420 TYR 0.007 0.001 TYR A 42 ARG 0.002 0.000 ARG B 456 Details of bonding type rmsd hydrogen bonds : bond 0.04395 ( 506) hydrogen bonds : angle 4.67459 ( 1452) covalent geometry : bond 0.00255 ( 8488) covalent geometry : angle 0.59065 (11588) Misc. bond : bond 0.00017 ( 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 120 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 1.295 Fit side-chains REVERT: A 161 MET cc_start: 0.9030 (mtp) cc_final: 0.8623 (mtm) REVERT: A 172 LEU cc_start: 0.8371 (tp) cc_final: 0.8007 (mt) REVERT: A 251 ILE cc_start: 0.7562 (OUTLIER) cc_final: 0.7252 (pt) REVERT: B 172 LEU cc_start: 0.8394 (tp) cc_final: 0.8028 (mt) REVERT: B 251 ILE cc_start: 0.7718 (OUTLIER) cc_final: 0.7394 (pt) REVERT: B 282 LYS cc_start: 0.7929 (mtmm) cc_final: 0.7460 (mtpm) REVERT: B 520 GLU cc_start: 0.7648 (mp0) cc_final: 0.7357 (mp0) outliers start: 12 outliers final: 9 residues processed: 111 average time/residue: 1.5459 time to fit residues: 184.3316 Evaluate side-chains 115 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.857 ------------------------------------------------------------------------------- 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 B residue 119 LYS 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 74 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 = 0.3664 r_free = 0.3664 target = 0.150831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.116034 restraints weight = 8203.358| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.18 r_work: 0.3084 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2355 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= 0.173 Angle : 0.663 9.351 11588 Z= 0.322 Chirality : 0.044 0.155 1422 Planarity : 0.005 0.043 1352 Dihedral : 12.601 134.358 1940 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.67 % Allowed : 17.74 % 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: 1.61 (0.19), residues: 666 sheet: None (None), residues: 0 loop : 1.31 (0.38), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 149 HIS 0.002 0.001 HIS A 354 PHE 0.020 0.002 PHE A 420 TYR 0.012 0.002 TYR A 42 ARG 0.006 0.001 ARG B 456 Details of bonding type rmsd hydrogen bonds : bond 0.05405 ( 506) hydrogen bonds : angle 4.88437 ( 1452) covalent geometry : bond 0.00405 ( 8488) covalent geometry : angle 0.66312 (11588) Misc. bond : bond 0.00019 ( 2) =============================================================================== Job complete usr+sys time: 6519.84 seconds wall clock time: 112 minutes 59.38 seconds (6779.38 seconds total)