Starting phenix.real_space_refine on Wed Mar 12 23:34:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uvf_42618/03_2025/8uvf_42618.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uvf_42618/03_2025/8uvf_42618.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uvf_42618/03_2025/8uvf_42618.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uvf_42618/03_2025/8uvf_42618.map" model { file = "/net/cci-nas-00/data/ceres_data/8uvf_42618/03_2025/8uvf_42618.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uvf_42618/03_2025/8uvf_42618.cif" } resolution = 2.17 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.042 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 4 5.49 5 S 52 5.16 5 Na 4 4.78 5 C 5818 2.51 5 N 1272 2.21 5 O 1370 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 8520 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4011 Classifications: {'peptide': 513} Link IDs: {'PTRANS': 34, 'TRANS': 478} Chain breaks: 2 Chain: "A" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 249 Unusual residues: {' NA': 2, '3PE': 2, 'C14': 3, 'CLR': 4} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Restraints were copied for chains: B Time building chain proxies: 8.76, per 1000 atoms: 1.03 Number of scatterers: 8520 At special positions: 0 Unit cell: (84.975, 110.55, 82.5, 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 52 16.00 P 4 15.00 Na 4 11.00 O 1370 8.00 N 1272 7.00 C 5818 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.52 Conformation dependent library (CDL) restraints added in 1.0 seconds 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1924 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 0 sheets defined 84.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 1 through 14 removed outlier: 3.614A pdb=" N ALA A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 34 Proline residue: A 24 - end of helix Proline residue: A 29 - end of helix removed outlier: 3.884A pdb=" N PHE A 32 " --> pdb=" O LEU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 54 Processing helix chain 'A' and resid 58 through 64 Processing helix chain 'A' and resid 64 through 73 removed outlier: 3.751A pdb=" N VAL A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Proline residue: A 71 - end of helix Processing helix chain 'A' and resid 77 through 82 Processing helix chain 'A' and resid 83 through 86 Processing helix chain 'A' and resid 87 through 106 removed outlier: 3.676A pdb=" N PHE A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TRP A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 121 removed outlier: 3.613A pdb=" N GLY A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 140 Processing helix chain 'A' and resid 143 through 163 Proline residue: A 153 - end of helix Processing helix chain 'A' and resid 220 through 247 removed outlier: 3.656A pdb=" N ILE A 238 " --> pdb=" O PHE A 234 " (cutoff:3.500A) Proline residue: A 239 - end of helix removed outlier: 3.834A pdb=" N THR A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 267 removed outlier: 3.989A pdb=" N LEU A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 301 Proline residue: A 284 - end of helix Processing helix chain 'A' and resid 320 through 335 Processing helix chain 'A' and resid 339 through 359 Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 377 through 390 removed outlier: 3.796A pdb=" N ILE A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU A 389 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE A 390 " --> pdb=" O VAL A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 404 removed outlier: 3.907A pdb=" N PHE A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 425 Processing helix chain 'A' and resid 426 through 446 Processing helix chain 'A' and resid 447 through 456 Processing helix chain 'A' and resid 457 through 460 Processing helix chain 'A' and resid 463 through 479 Processing helix chain 'A' and resid 483 through 503 Proline residue: A 493 - end of helix Processing helix chain 'A' and resid 505 through 517 removed outlier: 3.833A pdb=" N LEU A 509 " --> pdb=" O HIS A 505 " (cutoff:3.500A) Proline residue: A 512 - end of helix Processing helix chain 'A' and resid 527 through 535 Processing helix chain 'A' and resid 540 through 566 removed outlier: 4.198A pdb=" N LEU A 550 " --> pdb=" O ARG A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 572 Processing helix chain 'A' and resid 577 through 581 Processing helix chain 'B' and resid 2 through 14 Processing helix chain 'B' and resid 14 through 34 Proline residue: B 24 - end of helix Proline residue: B 29 - end of helix removed outlier: 3.883A pdb=" N PHE B 32 " --> pdb=" O LEU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 54 Processing helix chain 'B' and resid 58 through 64 Processing helix chain 'B' and resid 64 through 73 removed outlier: 3.750A pdb=" N VAL B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Proline residue: B 71 - end of helix Processing helix chain 'B' and resid 77 through 82 Processing helix chain 'B' and resid 83 through 86 Processing helix chain 'B' and resid 87 through 106 removed outlier: 3.676A pdb=" N PHE B 91 " --> pdb=" O LEU B 87 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TRP B 106 " --> pdb=" O ALA B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 121 removed outlier: 3.614A pdb=" N GLY B 121 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 140 Processing helix chain 'B' and resid 143 through 163 Proline residue: B 153 - end of helix Processing helix chain 'B' and resid 220 through 247 removed outlier: 3.656A pdb=" N ILE B 238 " --> pdb=" O PHE B 234 " (cutoff:3.500A) Proline residue: B 239 - end of helix removed outlier: 3.835A pdb=" N THR B 247 " --> pdb=" O SER B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 267 removed outlier: 3.988A pdb=" N LEU B 257 " --> pdb=" O THR B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 301 Proline residue: B 284 - end of helix Processing helix chain 'B' and resid 320 through 335 Processing helix chain 'B' and resid 339 through 359 Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 377 through 390 removed outlier: 3.796A pdb=" N ILE B 388 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU B 389 " --> pdb=" O ILE B 385 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE B 390 " --> pdb=" O VAL B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 404 removed outlier: 3.907A pdb=" N PHE B 403 " --> pdb=" O LEU B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 425 Processing helix chain 'B' and resid 426 through 446 Processing helix chain 'B' and resid 447 through 456 Processing helix chain 'B' and resid 457 through 460 Processing helix chain 'B' and resid 463 through 479 Processing helix chain 'B' and resid 483 through 503 Proline residue: B 493 - end of helix Processing helix chain 'B' and resid 505 through 517 removed outlier: 3.833A pdb=" N LEU B 509 " --> pdb=" O HIS B 505 " (cutoff:3.500A) Proline residue: B 512 - end of helix Processing helix chain 'B' and resid 527 through 535 Processing helix chain 'B' and resid 540 through 566 removed outlier: 4.198A pdb=" N LEU B 550 " --> pdb=" O ARG B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 572 Processing helix chain 'B' and resid 577 through 581 556 hydrogen bonds defined for protein. 1626 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: 2.39 Time building geometry restraints manager: 2.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1208 1.30 - 1.43: 2184 1.43 - 1.55: 5264 1.55 - 1.68: 16 1.68 - 1.81: 90 Bond restraints: 8762 Sorted by residual: bond pdb=" C PRO A 83 " pdb=" O PRO A 83 " ideal model delta sigma weight residual 1.237 1.176 0.061 1.32e-02 5.74e+03 2.14e+01 bond pdb=" C PRO B 83 " pdb=" O PRO B 83 " ideal model delta sigma weight residual 1.237 1.177 0.061 1.32e-02 5.74e+03 2.12e+01 bond pdb=" C GLN A 84 " pdb=" O GLN A 84 " ideal model delta sigma weight residual 1.236 1.190 0.046 1.28e-02 6.10e+03 1.28e+01 bond pdb=" C GLN B 84 " pdb=" O GLN B 84 " ideal model delta sigma weight residual 1.236 1.191 0.045 1.28e-02 6.10e+03 1.25e+01 bond pdb=" C PHE A 86 " pdb=" O PHE A 86 " ideal model delta sigma weight residual 1.235 1.189 0.046 1.41e-02 5.03e+03 1.06e+01 ... (remaining 8757 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 11373 1.38 - 2.76: 403 2.76 - 4.13: 93 4.13 - 5.51: 39 5.51 - 6.89: 12 Bond angle restraints: 11920 Sorted by residual: angle pdb=" CA LEU B 87 " pdb=" C LEU B 87 " pdb=" O LEU B 87 " ideal model delta sigma weight residual 121.87 114.98 6.89 1.10e+00 8.26e-01 3.92e+01 angle pdb=" CA LEU A 87 " pdb=" C LEU A 87 " pdb=" O LEU A 87 " ideal model delta sigma weight residual 121.87 114.99 6.88 1.10e+00 8.26e-01 3.92e+01 angle pdb=" CA LEU A 87 " pdb=" C LEU A 87 " pdb=" N ASP A 88 " ideal model delta sigma weight residual 115.30 121.99 -6.69 1.33e+00 5.65e-01 2.53e+01 angle pdb=" CA LEU B 87 " pdb=" C LEU B 87 " pdb=" N ASP B 88 " ideal model delta sigma weight residual 115.30 121.97 -6.67 1.33e+00 5.65e-01 2.51e+01 angle pdb=" O CYS A 82 " pdb=" C CYS A 82 " pdb=" N PRO A 83 " ideal model delta sigma weight residual 120.71 117.45 3.26 9.40e-01 1.13e+00 1.20e+01 ... (remaining 11915 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.85: 5350 24.85 - 49.71: 162 49.71 - 74.56: 37 74.56 - 99.41: 25 99.41 - 124.27: 8 Dihedral angle restraints: 5582 sinusoidal: 2624 harmonic: 2958 Sorted by residual: dihedral pdb=" C PHE B 86 " pdb=" N PHE B 86 " pdb=" CA PHE B 86 " pdb=" CB PHE B 86 " ideal model delta harmonic sigma weight residual -122.60 -135.99 13.39 0 2.50e+00 1.60e-01 2.87e+01 dihedral pdb=" C PHE A 86 " pdb=" N PHE A 86 " pdb=" CA PHE A 86 " pdb=" CB PHE A 86 " ideal model delta harmonic sigma weight residual -122.60 -135.98 13.38 0 2.50e+00 1.60e-01 2.86e+01 dihedral pdb=" N PHE B 86 " pdb=" C PHE B 86 " pdb=" CA PHE B 86 " pdb=" CB PHE B 86 " ideal model delta harmonic sigma weight residual 122.80 134.36 -11.56 0 2.50e+00 1.60e-01 2.14e+01 ... (remaining 5579 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1323 0.098 - 0.195: 61 0.195 - 0.293: 2 0.293 - 0.390: 2 0.390 - 0.488: 2 Chirality restraints: 1390 Sorted by residual: chirality pdb=" CA PHE B 86 " pdb=" N PHE B 86 " pdb=" C PHE B 86 " pdb=" CB PHE B 86 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.94e+00 chirality pdb=" CA PHE A 86 " pdb=" N PHE A 86 " pdb=" C PHE A 86 " pdb=" CB PHE A 86 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.92e+00 chirality pdb=" CA LEU B 87 " pdb=" N LEU B 87 " pdb=" C LEU B 87 " pdb=" CB LEU B 87 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.41e+00 ... (remaining 1387 not shown) Planarity restraints: 1384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS B 82 " -0.011 2.00e-02 2.50e+03 2.04e-02 4.16e+00 pdb=" C CYS B 82 " 0.035 2.00e-02 2.50e+03 pdb=" O CYS B 82 " -0.012 2.00e-02 2.50e+03 pdb=" N PRO B 83 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 82 " 0.011 2.00e-02 2.50e+03 2.04e-02 4.15e+00 pdb=" C CYS A 82 " -0.035 2.00e-02 2.50e+03 pdb=" O CYS A 82 " 0.012 2.00e-02 2.50e+03 pdb=" N PRO A 83 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 527 " 0.028 5.00e-02 4.00e+02 4.24e-02 2.88e+00 pdb=" N PRO B 528 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 528 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 528 " 0.023 5.00e-02 4.00e+02 ... (remaining 1381 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 605 2.74 - 3.28: 8786 3.28 - 3.82: 15290 3.82 - 4.36: 18000 4.36 - 4.90: 31043 Nonbonded interactions: 73724 Sorted by model distance: nonbonded pdb=" O LEU B 561 " pdb=" OG1 THR B 565 " model vdw 2.198 3.040 nonbonded pdb=" O LEU A 561 " pdb=" OG1 THR A 565 " model vdw 2.198 3.040 nonbonded pdb=" OD1 ASN B 484 " pdb="NA NA B 702 " model vdw 2.289 2.470 nonbonded pdb=" OD1 ASN A 484 " pdb="NA NA A 702 " model vdw 2.290 2.470 nonbonded pdb=" NZ LYS A 10 " pdb=" O TRP B 401 " model vdw 2.293 3.120 ... (remaining 73719 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: 2.670 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.540 Find NCS groups from input model: 0.140 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:13.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 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 : 0.005 0.061 8762 Z= 0.303 Angle : 0.675 6.889 11920 Z= 0.357 Chirality : 0.049 0.488 1390 Planarity : 0.006 0.057 1384 Dihedral : 15.064 124.265 3658 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 0.47 % Allowed : 0.70 % Favored : 98.84 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.27), residues: 1014 helix: 1.77 (0.19), residues: 784 sheet: None (None), residues: 0 loop : 0.52 (0.45), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 418 HIS 0.008 0.002 HIS A 457 PHE 0.028 0.002 PHE A 363 TYR 0.017 0.002 TYR B 85 ARG 0.003 0.001 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 142 time to evaluate : 0.919 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 144 average time/residue: 1.4272 time to fit residues: 217.7157 Evaluate side-chains 119 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 117 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain B residue 86 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 41 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 457 HIS B 538 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.153825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.114124 restraints weight = 7744.273| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.41 r_work: 0.3261 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8762 Z= 0.204 Angle : 0.613 8.467 11920 Z= 0.296 Chirality : 0.043 0.140 1390 Planarity : 0.005 0.046 1384 Dihedral : 11.461 88.956 1836 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.81 % Allowed : 4.88 % Favored : 94.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.27), residues: 1014 helix: 1.82 (0.18), residues: 790 sheet: None (None), residues: 0 loop : 0.44 (0.47), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 418 HIS 0.011 0.003 HIS B 457 PHE 0.020 0.002 PHE B 363 TYR 0.011 0.001 TYR B 226 ARG 0.004 0.001 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 125 time to evaluate : 0.858 Fit side-chains revert: symmetry clash REVERT: B 123 GLN cc_start: 0.7977 (mp10) cc_final: 0.7694 (mp-120) REVERT: B 510 MET cc_start: 0.9068 (mtp) cc_final: 0.8757 (mtp) outliers start: 7 outliers final: 3 residues processed: 128 average time/residue: 1.1617 time to fit residues: 158.7450 Evaluate side-chains 118 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 115 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 525 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 26 optimal weight: 4.9990 chunk 35 optimal weight: 0.4980 chunk 82 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 57 optimal weight: 0.5980 chunk 85 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 HIS A 538 HIS B 457 HIS B 538 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.151447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.111560 restraints weight = 7874.619| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.41 r_work: 0.3231 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8762 Z= 0.223 Angle : 0.587 7.180 11920 Z= 0.291 Chirality : 0.043 0.154 1390 Planarity : 0.005 0.045 1384 Dihedral : 10.344 88.023 1836 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 0.93 % Allowed : 6.86 % Favored : 92.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.27), residues: 1014 helix: 1.85 (0.18), residues: 790 sheet: None (None), residues: 0 loop : 0.45 (0.47), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 418 HIS 0.017 0.004 HIS A 538 PHE 0.018 0.002 PHE A 352 TYR 0.008 0.001 TYR B 226 ARG 0.006 0.001 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 0.852 Fit side-chains revert: symmetry clash REVERT: B 86 PHE cc_start: 0.8846 (OUTLIER) cc_final: 0.7535 (t80) REVERT: B 123 GLN cc_start: 0.7977 (mp10) cc_final: 0.7708 (mp-120) REVERT: B 151 MET cc_start: 0.8681 (mmm) cc_final: 0.8250 (mmm) REVERT: B 445 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7242 (mp0) outliers start: 8 outliers final: 3 residues processed: 122 average time/residue: 1.1262 time to fit residues: 147.2641 Evaluate side-chains 116 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 111 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 525 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 30 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 5 optimal weight: 0.4980 chunk 91 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 HIS B 457 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.151680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.112035 restraints weight = 7860.104| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.41 r_work: 0.3232 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8762 Z= 0.199 Angle : 0.557 7.104 11920 Z= 0.277 Chirality : 0.042 0.164 1390 Planarity : 0.005 0.045 1384 Dihedral : 10.385 88.483 1836 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.28 % Allowed : 8.14 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.27), residues: 1014 helix: 1.92 (0.18), residues: 790 sheet: None (None), residues: 0 loop : 0.42 (0.47), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 418 HIS 0.019 0.003 HIS A 457 PHE 0.019 0.001 PHE A 352 TYR 0.007 0.001 TYR B 226 ARG 0.007 0.001 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.906 Fit side-chains revert: symmetry clash REVERT: A 413 GLU cc_start: 0.7120 (tp30) cc_final: 0.6081 (tm-30) REVERT: A 445 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7221 (mp0) REVERT: B 86 PHE cc_start: 0.8808 (OUTLIER) cc_final: 0.7488 (t80) REVERT: B 123 GLN cc_start: 0.8025 (mp10) cc_final: 0.7760 (mp-120) REVERT: B 151 MET cc_start: 0.8688 (mmm) cc_final: 0.8237 (mmm) REVERT: B 500 ILE cc_start: 0.8735 (mm) cc_final: 0.8535 (mt) outliers start: 11 outliers final: 4 residues processed: 119 average time/residue: 1.0804 time to fit residues: 138.4250 Evaluate side-chains 117 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 111 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 231 TRP Chi-restraints excluded: chain B residue 525 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 92 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 34 optimal weight: 0.0050 chunk 26 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN A 457 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.145338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.105009 restraints weight = 7735.440| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.38 r_work: 0.3130 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8762 Z= 0.280 Angle : 0.611 7.537 11920 Z= 0.304 Chirality : 0.045 0.174 1390 Planarity : 0.006 0.048 1384 Dihedral : 10.773 88.181 1836 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.51 % Allowed : 8.95 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.27), residues: 1014 helix: 1.77 (0.18), residues: 790 sheet: None (None), residues: 0 loop : 0.44 (0.47), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 418 HIS 0.020 0.003 HIS A 457 PHE 0.020 0.002 PHE A 352 TYR 0.009 0.001 TYR B 332 ARG 0.010 0.001 ARG B 227 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.834 Fit side-chains revert: symmetry clash REVERT: A 413 GLU cc_start: 0.7152 (tp30) cc_final: 0.6091 (tm-30) REVERT: B 86 PHE cc_start: 0.8836 (OUTLIER) cc_final: 0.7433 (t80) REVERT: B 123 GLN cc_start: 0.7989 (mp10) cc_final: 0.7708 (mp-120) REVERT: B 151 MET cc_start: 0.8630 (mmm) cc_final: 0.8222 (mmm) REVERT: B 231 TRP cc_start: 0.8573 (OUTLIER) cc_final: 0.7932 (t-100) outliers start: 13 outliers final: 4 residues processed: 123 average time/residue: 1.0014 time to fit residues: 132.9564 Evaluate side-chains 116 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 231 TRP Chi-restraints excluded: chain B residue 525 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 59 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN A 457 HIS A 538 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.147003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.106894 restraints weight = 7717.528| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.39 r_work: 0.3160 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8762 Z= 0.198 Angle : 0.560 7.648 11920 Z= 0.278 Chirality : 0.042 0.182 1390 Planarity : 0.006 0.049 1384 Dihedral : 10.516 89.095 1836 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 1.28 % Allowed : 9.77 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.27), residues: 1014 helix: 1.88 (0.18), residues: 790 sheet: None (None), residues: 0 loop : 0.34 (0.46), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 418 HIS 0.020 0.003 HIS A 457 PHE 0.019 0.001 PHE A 352 TYR 0.006 0.001 TYR B 226 ARG 0.011 0.001 ARG B 227 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.867 Fit side-chains revert: symmetry clash REVERT: A 413 GLU cc_start: 0.7209 (tp30) cc_final: 0.6165 (tm-30) REVERT: A 445 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7203 (mp0) REVERT: B 86 PHE cc_start: 0.8782 (OUTLIER) cc_final: 0.7454 (t80) REVERT: B 123 GLN cc_start: 0.7929 (mp10) cc_final: 0.7650 (mp-120) REVERT: B 150 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.7786 (ttm) REVERT: B 151 MET cc_start: 0.8614 (mmm) cc_final: 0.8174 (mmm) REVERT: B 227 ARG cc_start: 0.7078 (mtp-110) cc_final: 0.6638 (ttp-110) REVERT: B 231 TRP cc_start: 0.8566 (OUTLIER) cc_final: 0.7939 (t-100) REVERT: B 338 ILE cc_start: 0.7968 (OUTLIER) cc_final: 0.7347 (mt) outliers start: 11 outliers final: 2 residues processed: 121 average time/residue: 1.0287 time to fit residues: 134.6580 Evaluate side-chains 114 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 231 TRP Chi-restraints excluded: chain B residue 338 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 11 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 97 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN A 457 HIS A 538 HIS B 457 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.146653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.106568 restraints weight = 7758.010| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.39 r_work: 0.3148 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8762 Z= 0.204 Angle : 0.559 7.168 11920 Z= 0.279 Chirality : 0.042 0.192 1390 Planarity : 0.006 0.052 1384 Dihedral : 10.410 89.453 1836 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.74 % Allowed : 10.00 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.27), residues: 1014 helix: 1.86 (0.18), residues: 792 sheet: None (None), residues: 0 loop : 0.34 (0.47), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 418 HIS 0.018 0.004 HIS A 457 PHE 0.019 0.002 PHE A 352 TYR 0.007 0.001 TYR B 332 ARG 0.012 0.001 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: A 55 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7523 (mt-10) REVERT: A 86 PHE cc_start: 0.8718 (OUTLIER) cc_final: 0.7052 (t80) REVERT: A 338 ILE cc_start: 0.7875 (OUTLIER) cc_final: 0.7251 (mt) REVERT: A 413 GLU cc_start: 0.7405 (tp30) cc_final: 0.6317 (tm-30) REVERT: A 445 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7255 (mp0) REVERT: B 86 PHE cc_start: 0.8790 (OUTLIER) cc_final: 0.7468 (t80) REVERT: B 123 GLN cc_start: 0.7937 (mp10) cc_final: 0.7684 (mp-120) REVERT: B 150 MET cc_start: 0.8561 (OUTLIER) cc_final: 0.7807 (ttm) REVERT: B 151 MET cc_start: 0.8622 (mmm) cc_final: 0.8169 (mmm) REVERT: B 231 TRP cc_start: 0.8559 (OUTLIER) cc_final: 0.7985 (t-100) REVERT: B 338 ILE cc_start: 0.7989 (OUTLIER) cc_final: 0.7353 (mt) outliers start: 15 outliers final: 3 residues processed: 117 average time/residue: 1.0743 time to fit residues: 135.6883 Evaluate side-chains 119 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 231 TRP Chi-restraints excluded: chain B residue 338 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 75 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 72 optimal weight: 0.0270 chunk 59 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN A 457 HIS A 538 HIS B 457 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.147573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.107499 restraints weight = 7931.828| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.40 r_work: 0.3167 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8762 Z= 0.182 Angle : 0.547 6.990 11920 Z= 0.273 Chirality : 0.042 0.193 1390 Planarity : 0.006 0.059 1384 Dihedral : 10.301 89.622 1836 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 1.40 % Allowed : 10.47 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.34 (0.27), residues: 1014 helix: 1.92 (0.18), residues: 792 sheet: None (None), residues: 0 loop : 0.31 (0.46), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 418 HIS 0.018 0.003 HIS A 457 PHE 0.018 0.001 PHE A 352 TYR 0.006 0.001 TYR B 226 ARG 0.012 0.001 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 1.065 Fit side-chains revert: symmetry clash REVERT: A 86 PHE cc_start: 0.8675 (OUTLIER) cc_final: 0.7000 (t80) REVERT: A 227 ARG cc_start: 0.7270 (mtp-110) cc_final: 0.6798 (ttp-110) REVERT: A 413 GLU cc_start: 0.7294 (tp30) cc_final: 0.6247 (tm-30) REVERT: A 445 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7214 (mp0) REVERT: B 86 PHE cc_start: 0.8767 (OUTLIER) cc_final: 0.7415 (t80) REVERT: B 123 GLN cc_start: 0.7910 (mp10) cc_final: 0.7660 (mp-120) REVERT: B 150 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.7766 (ttm) REVERT: B 227 ARG cc_start: 0.7045 (mtp-110) cc_final: 0.6582 (ttp-110) REVERT: B 231 TRP cc_start: 0.8542 (OUTLIER) cc_final: 0.7974 (t-100) REVERT: B 338 ILE cc_start: 0.7954 (OUTLIER) cc_final: 0.7326 (mt) outliers start: 12 outliers final: 2 residues processed: 121 average time/residue: 1.0540 time to fit residues: 137.7930 Evaluate side-chains 118 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 231 TRP Chi-restraints excluded: chain B residue 338 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 11 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 5 optimal weight: 0.0470 chunk 101 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.7880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN A 457 HIS B 457 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.147089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.107029 restraints weight = 7850.228| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.39 r_work: 0.3159 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8762 Z= 0.194 Angle : 0.554 7.103 11920 Z= 0.276 Chirality : 0.042 0.193 1390 Planarity : 0.006 0.053 1384 Dihedral : 10.354 89.078 1836 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.40 % Allowed : 10.70 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.27), residues: 1014 helix: 1.90 (0.18), residues: 792 sheet: None (None), residues: 0 loop : 0.30 (0.46), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 418 HIS 0.019 0.003 HIS A 457 PHE 0.019 0.001 PHE A 352 TYR 0.006 0.001 TYR B 332 ARG 0.011 0.001 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.852 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.2830 (tpt) cc_final: 0.2514 (tpt) REVERT: A 86 PHE cc_start: 0.8691 (OUTLIER) cc_final: 0.6897 (t80) REVERT: A 338 ILE cc_start: 0.7841 (OUTLIER) cc_final: 0.7223 (mt) REVERT: A 413 GLU cc_start: 0.7336 (tp30) cc_final: 0.6305 (tm-30) REVERT: A 445 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7225 (mp0) REVERT: B 86 PHE cc_start: 0.8773 (OUTLIER) cc_final: 0.7435 (t80) REVERT: B 123 GLN cc_start: 0.7917 (mp10) cc_final: 0.7659 (mp-120) REVERT: B 150 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.7777 (ttm) REVERT: B 151 MET cc_start: 0.8617 (mmm) cc_final: 0.8160 (mmm) REVERT: B 227 ARG cc_start: 0.7004 (mtp-110) cc_final: 0.6587 (ttp-110) REVERT: B 231 TRP cc_start: 0.8541 (OUTLIER) cc_final: 0.7973 (t-100) REVERT: B 338 ILE cc_start: 0.7965 (OUTLIER) cc_final: 0.7333 (mt) outliers start: 12 outliers final: 3 residues processed: 119 average time/residue: 1.0923 time to fit residues: 139.8393 Evaluate side-chains 121 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 231 TRP Chi-restraints excluded: chain B residue 338 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 68 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 84 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN A 457 HIS B 457 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.144043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.103782 restraints weight = 7791.103| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.39 r_work: 0.3113 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 8762 Z= 0.310 Angle : 0.648 7.510 11920 Z= 0.323 Chirality : 0.047 0.203 1390 Planarity : 0.006 0.058 1384 Dihedral : 10.998 88.125 1836 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.40 % Allowed : 10.58 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.27), residues: 1014 helix: 1.66 (0.18), residues: 790 sheet: None (None), residues: 0 loop : 0.36 (0.46), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 418 HIS 0.017 0.004 HIS A 457 PHE 0.021 0.002 PHE A 352 TYR 0.009 0.001 TYR B 332 ARG 0.016 0.001 ARG A 227 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.2800 (tpt) cc_final: 0.2474 (tpt) REVERT: A 55 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7673 (mt-10) REVERT: A 227 ARG cc_start: 0.7322 (mtp-110) cc_final: 0.6805 (ttp-110) REVERT: A 413 GLU cc_start: 0.7402 (tp30) cc_final: 0.6376 (tm-30) REVERT: B 123 GLN cc_start: 0.7991 (mp10) cc_final: 0.7651 (mp-120) REVERT: B 151 MET cc_start: 0.8640 (mmm) cc_final: 0.8158 (mmm) REVERT: B 231 TRP cc_start: 0.8566 (OUTLIER) cc_final: 0.7937 (t-100) REVERT: B 338 ILE cc_start: 0.8056 (OUTLIER) cc_final: 0.7391 (mt) outliers start: 12 outliers final: 5 residues processed: 119 average time/residue: 1.2162 time to fit residues: 155.0552 Evaluate side-chains 117 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 231 TRP Chi-restraints excluded: chain B residue 338 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 63 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 67 optimal weight: 0.1980 chunk 100 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 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 229 ASN A 457 HIS B 457 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.146791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.106823 restraints weight = 7876.810| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.40 r_work: 0.3156 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8762 Z= 0.189 Angle : 0.559 7.051 11920 Z= 0.278 Chirality : 0.042 0.199 1390 Planarity : 0.006 0.060 1384 Dihedral : 10.658 89.187 1836 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 1.28 % Allowed : 11.05 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.27), residues: 1014 helix: 1.84 (0.18), residues: 792 sheet: None (None), residues: 0 loop : 0.31 (0.46), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 418 HIS 0.018 0.003 HIS A 457 PHE 0.018 0.001 PHE A 352 TYR 0.007 0.001 TYR B 226 ARG 0.014 0.001 ARG A 227 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8081.64 seconds wall clock time: 139 minutes 31.84 seconds (8371.84 seconds total)