Starting phenix.real_space_refine on Fri Aug 22 22:46:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uvf_42618/08_2025/8uvf_42618.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uvf_42618/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8uvf_42618/08_2025/8uvf_42618.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uvf_42618/08_2025/8uvf_42618.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8uvf_42618/08_2025/8uvf_42618.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uvf_42618/08_2025/8uvf_42618.map" } resolution = 2.17 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 3.04, per 1000 atoms: 0.36 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: 0.60 Conformation dependent library (CDL) restraints added in 279.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.17 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: 0.88 Time building geometry restraints manager: 0.75 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.370 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.660 ------------------------------------------------------------------------------- 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= 0.256 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 ARG 0.003 0.001 ARG A 228 TYR 0.017 0.002 TYR B 85 PHE 0.028 0.002 PHE A 363 TRP 0.020 0.001 TRP B 418 HIS 0.008 0.002 HIS A 457 Details of bonding type rmsd covalent geometry : bond 0.00477 ( 8762) covalent geometry : angle 0.67533 (11920) hydrogen bonds : bond 0.12006 ( 556) hydrogen bonds : angle 4.64040 ( 1626) *********************** 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 : 0.225 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 144 average time/residue: 0.5854 time to fit residues: 89.0370 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 : 0.302 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.0370 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 overall best weight: 0.5858 ------------------------------------------------------------------------------- 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 = 0.3885 r_free = 0.3885 target = 0.154766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.115150 restraints weight = 7817.023| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.42 r_work: 0.3275 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8762 Z= 0.131 Angle : 0.600 8.494 11920 Z= 0.290 Chirality : 0.042 0.139 1390 Planarity : 0.005 0.046 1384 Dihedral : 11.362 88.928 1836 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 0.58 % Allowed : 5.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.33 (0.27), residues: 1014 helix: 1.88 (0.18), residues: 788 sheet: None (None), residues: 0 loop : 0.52 (0.47), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 15 TYR 0.010 0.001 TYR B 226 PHE 0.020 0.001 PHE B 363 TRP 0.019 0.002 TRP A 418 HIS 0.012 0.003 HIS B 538 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 8762) covalent geometry : angle 0.60026 (11920) hydrogen bonds : bond 0.04024 ( 556) hydrogen bonds : angle 3.99785 ( 1626) *********************** 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 127 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 122 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: B 123 GLN cc_start: 0.7911 (mp10) cc_final: 0.7696 (mp-120) REVERT: B 151 MET cc_start: 0.8715 (mmm) cc_final: 0.8326 (mmm) outliers start: 5 outliers final: 3 residues processed: 125 average time/residue: 0.5046 time to fit residues: 67.1998 Evaluate side-chains 116 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 113 time to evaluate : 0.263 ------------------------------------------------------------------------------- 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 64 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 22 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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 = 0.3839 r_free = 0.3839 target = 0.150580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.110669 restraints weight = 7752.122| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.40 r_work: 0.3217 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8762 Z= 0.170 Angle : 0.607 7.355 11920 Z= 0.303 Chirality : 0.045 0.155 1390 Planarity : 0.006 0.045 1384 Dihedral : 10.424 87.624 1836 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.05 % Allowed : 6.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.20 (0.27), residues: 1014 helix: 1.78 (0.18), residues: 790 sheet: None (None), residues: 0 loop : 0.48 (0.47), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 227 TYR 0.008 0.001 TYR B 332 PHE 0.019 0.002 PHE A 352 TRP 0.026 0.002 TRP A 418 HIS 0.016 0.004 HIS A 538 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 8762) covalent geometry : angle 0.60737 (11920) hydrogen bonds : bond 0.04543 ( 556) hydrogen bonds : angle 4.15511 ( 1626) *********************** 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 128 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: B 86 PHE cc_start: 0.8858 (OUTLIER) cc_final: 0.7570 (t80) REVERT: B 123 GLN cc_start: 0.7988 (mp10) cc_final: 0.7703 (mp-120) REVERT: B 151 MET cc_start: 0.8693 (mmm) cc_final: 0.8187 (mmm) REVERT: B 445 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7238 (mp0) outliers start: 9 outliers final: 3 residues processed: 122 average time/residue: 0.4761 time to fit residues: 62.0848 Evaluate side-chains 117 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 112 time to evaluate : 0.190 ------------------------------------------------------------------------------- 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 150 MET 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 15 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 33 optimal weight: 9.9990 chunk 76 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.150180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.110689 restraints weight = 7893.708| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.38 r_work: 0.3218 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8762 Z= 0.157 Angle : 0.592 7.442 11920 Z= 0.294 Chirality : 0.044 0.164 1390 Planarity : 0.006 0.048 1384 Dihedral : 10.577 88.113 1836 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.40 % Allowed : 8.26 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.19 (0.27), residues: 1014 helix: 1.80 (0.18), residues: 790 sheet: None (None), residues: 0 loop : 0.38 (0.47), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 227 TYR 0.007 0.001 TYR B 332 PHE 0.019 0.002 PHE A 352 TRP 0.026 0.002 TRP A 418 HIS 0.017 0.004 HIS A 457 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 8762) covalent geometry : angle 0.59182 (11920) hydrogen bonds : bond 0.04243 ( 556) hydrogen bonds : angle 4.08981 ( 1626) *********************** 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 125 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: A 231 TRP cc_start: 0.8697 (OUTLIER) cc_final: 0.8376 (t-100) REVERT: A 413 GLU cc_start: 0.7165 (tp30) cc_final: 0.6160 (tm-30) REVERT: A 546 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7926 (ptt-90) REVERT: B 86 PHE cc_start: 0.8835 (OUTLIER) cc_final: 0.7521 (t80) REVERT: B 123 GLN cc_start: 0.8056 (mp10) cc_final: 0.7797 (mp-120) REVERT: B 151 MET cc_start: 0.8691 (mmm) cc_final: 0.8210 (mmm) REVERT: B 231 TRP cc_start: 0.8642 (OUTLIER) cc_final: 0.7991 (t-100) outliers start: 12 outliers final: 3 residues processed: 121 average time/residue: 0.4562 time to fit residues: 59.0876 Evaluate side-chains 115 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 108 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain A residue 546 ARG 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 525 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 46 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 16 optimal weight: 0.4980 chunk 18 optimal weight: 0.5980 chunk 79 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3785 r_free = 0.3785 target = 0.147471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.107279 restraints weight = 7852.197| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.40 r_work: 0.3164 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8762 Z= 0.131 Angle : 0.551 7.151 11920 Z= 0.274 Chirality : 0.042 0.173 1390 Planarity : 0.005 0.050 1384 Dihedral : 10.506 89.136 1836 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.63 % Allowed : 9.19 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.32 (0.27), residues: 1014 helix: 1.91 (0.18), residues: 792 sheet: None (None), residues: 0 loop : 0.32 (0.47), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 227 TYR 0.005 0.001 TYR B 332 PHE 0.019 0.001 PHE A 352 TRP 0.025 0.002 TRP A 418 HIS 0.020 0.003 HIS A 457 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 8762) covalent geometry : angle 0.55059 (11920) hydrogen bonds : bond 0.03900 ( 556) hydrogen bonds : angle 3.99491 ( 1626) *********************** 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: 14 poor density : 113 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: A 86 PHE cc_start: 0.8705 (OUTLIER) cc_final: 0.7136 (t80) REVERT: A 338 ILE cc_start: 0.7846 (OUTLIER) cc_final: 0.7226 (mt) REVERT: A 413 GLU cc_start: 0.7145 (tp30) cc_final: 0.6081 (tm-30) REVERT: A 445 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7210 (mp0) REVERT: B 86 PHE cc_start: 0.8775 (OUTLIER) cc_final: 0.7432 (t80) REVERT: B 123 GLN cc_start: 0.7953 (mp10) cc_final: 0.7688 (mp-120) REVERT: B 151 MET cc_start: 0.8632 (mmm) cc_final: 0.8141 (mmm) REVERT: B 546 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7833 (ptt-90) outliers start: 14 outliers final: 3 residues processed: 123 average time/residue: 0.4518 time to fit residues: 59.6895 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 : 0.299 ------------------------------------------------------------------------------- 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 445 GLU 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 525 VAL Chi-restraints excluded: chain B residue 546 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.3761 r_free = 0.3761 target = 0.145367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.105049 restraints weight = 7791.578| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.39 r_work: 0.3129 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8762 Z= 0.171 Angle : 0.609 7.673 11920 Z= 0.303 Chirality : 0.044 0.179 1390 Planarity : 0.006 0.049 1384 Dihedral : 10.677 88.431 1836 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.63 % Allowed : 9.42 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.15 (0.27), residues: 1014 helix: 1.78 (0.18), residues: 790 sheet: None (None), residues: 0 loop : 0.34 (0.47), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 227 TYR 0.009 0.001 TYR B 332 PHE 0.020 0.002 PHE A 352 TRP 0.028 0.002 TRP A 418 HIS 0.018 0.004 HIS A 457 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 8762) covalent geometry : angle 0.60902 (11920) hydrogen bonds : bond 0.04459 ( 556) hydrogen bonds : angle 4.16351 ( 1626) *********************** 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 127 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 413 GLU cc_start: 0.7288 (tp30) cc_final: 0.6226 (tm-30) REVERT: A 546 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7826 (ptt-90) REVERT: B 1 MET cc_start: 0.3042 (tpt) cc_final: 0.2820 (tpt) REVERT: B 86 PHE cc_start: 0.8811 (OUTLIER) cc_final: 0.7394 (t80) REVERT: B 123 GLN cc_start: 0.7939 (mp10) cc_final: 0.7649 (mp-120) REVERT: B 151 MET cc_start: 0.8640 (mmm) cc_final: 0.8172 (mmm) REVERT: B 227 ARG cc_start: 0.7087 (mtp-110) cc_final: 0.6629 (ttp-110) REVERT: B 231 TRP cc_start: 0.8568 (OUTLIER) cc_final: 0.8005 (t-100) REVERT: B 338 ILE cc_start: 0.8016 (OUTLIER) cc_final: 0.7385 (mt) outliers start: 14 outliers final: 4 residues processed: 120 average time/residue: 0.4336 time to fit residues: 55.7704 Evaluate side-chains 116 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.209 ------------------------------------------------------------------------------- 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 546 ARG 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 Chi-restraints excluded: chain B residue 525 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 80 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 59 optimal weight: 0.2980 chunk 15 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 34 optimal weight: 0.0670 chunk 24 optimal weight: 5.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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 = 0.3789 r_free = 0.3789 target = 0.147953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.107858 restraints weight = 7912.217| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.40 r_work: 0.3171 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8762 Z= 0.117 Angle : 0.538 6.932 11920 Z= 0.267 Chirality : 0.041 0.187 1390 Planarity : 0.005 0.051 1384 Dihedral : 10.329 89.995 1836 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 1.16 % Allowed : 10.12 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.39 (0.27), residues: 1014 helix: 1.96 (0.18), residues: 792 sheet: None (None), residues: 0 loop : 0.34 (0.47), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 227 TYR 0.005 0.001 TYR A 240 PHE 0.018 0.001 PHE A 352 TRP 0.024 0.002 TRP B 418 HIS 0.018 0.003 HIS A 457 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 8762) covalent geometry : angle 0.53753 (11920) hydrogen bonds : bond 0.03652 ( 556) hydrogen bonds : angle 3.95149 ( 1626) *********************** 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 124 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: A 86 PHE cc_start: 0.8666 (OUTLIER) cc_final: 0.6941 (t80) REVERT: A 413 GLU cc_start: 0.7307 (tp30) cc_final: 0.6224 (tm-30) REVERT: A 445 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7203 (mp0) REVERT: B 86 PHE cc_start: 0.8756 (OUTLIER) cc_final: 0.7392 (t80) REVERT: B 123 GLN cc_start: 0.7899 (mp10) cc_final: 0.7618 (mp-120) REVERT: B 151 MET cc_start: 0.8619 (mmm) cc_final: 0.8111 (mmm) REVERT: B 231 TRP cc_start: 0.8543 (OUTLIER) cc_final: 0.7952 (t-100) REVERT: B 338 ILE cc_start: 0.7956 (OUTLIER) cc_final: 0.7327 (mt) outliers start: 10 outliers final: 2 residues processed: 120 average time/residue: 0.4524 time to fit residues: 58.4293 Evaluate side-chains 116 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 109 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 34 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 44 optimal weight: 0.4980 chunk 48 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3767 r_free = 0.3767 target = 0.145943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.105848 restraints weight = 7814.273| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.39 r_work: 0.3136 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8762 Z= 0.151 Angle : 0.582 7.272 11920 Z= 0.290 Chirality : 0.043 0.183 1390 Planarity : 0.006 0.060 1384 Dihedral : 10.471 89.585 1836 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.51 % Allowed : 10.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.28 (0.27), residues: 1014 helix: 1.87 (0.18), residues: 790 sheet: None (None), residues: 0 loop : 0.37 (0.46), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 227 TYR 0.008 0.001 TYR B 332 PHE 0.019 0.002 PHE A 352 TRP 0.026 0.002 TRP A 418 HIS 0.018 0.003 HIS A 457 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 8762) covalent geometry : angle 0.58197 (11920) hydrogen bonds : bond 0.04198 ( 556) hydrogen bonds : angle 4.08263 ( 1626) *********************** 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 121 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: A 86 PHE cc_start: 0.8735 (OUTLIER) cc_final: 0.6965 (t80) REVERT: A 227 ARG cc_start: 0.7306 (mtp-110) cc_final: 0.6796 (ttp-110) REVERT: A 413 GLU cc_start: 0.7412 (tp30) cc_final: 0.6399 (tm-30) REVERT: A 445 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7271 (mp0) REVERT: B 86 PHE cc_start: 0.8805 (OUTLIER) cc_final: 0.7375 (t80) REVERT: B 123 GLN cc_start: 0.7937 (mp10) cc_final: 0.7679 (mp-120) REVERT: B 151 MET cc_start: 0.8628 (mmm) cc_final: 0.8228 (mmm) REVERT: B 227 ARG cc_start: 0.7089 (mtp-110) cc_final: 0.6598 (ttp-110) REVERT: B 231 TRP cc_start: 0.8557 (OUTLIER) cc_final: 0.7972 (t-100) REVERT: B 338 ILE cc_start: 0.8020 (OUTLIER) cc_final: 0.7380 (mt) REVERT: B 546 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7906 (ptt-90) outliers start: 13 outliers final: 3 residues processed: 114 average time/residue: 0.4730 time to fit residues: 57.9291 Evaluate side-chains 117 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU 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 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 Chi-restraints excluded: chain B residue 546 ARG 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 37 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 29 optimal weight: 0.3980 chunk 100 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 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 = 0.3780 r_free = 0.3780 target = 0.147146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.107125 restraints weight = 7824.365| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.39 r_work: 0.3162 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2131 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= 0.127 Angle : 0.552 7.067 11920 Z= 0.275 Chirality : 0.042 0.187 1390 Planarity : 0.006 0.051 1384 Dihedral : 10.403 89.399 1836 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 1.28 % Allowed : 10.47 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.35 (0.27), residues: 1014 helix: 1.93 (0.18), residues: 792 sheet: None (None), residues: 0 loop : 0.34 (0.46), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 227 TYR 0.006 0.001 TYR B 332 PHE 0.018 0.001 PHE A 352 TRP 0.025 0.002 TRP A 418 HIS 0.017 0.003 HIS A 457 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 8762) covalent geometry : angle 0.55215 (11920) hydrogen bonds : bond 0.03823 ( 556) hydrogen bonds : angle 3.98552 ( 1626) *********************** 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 119 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.2770 (tpt) cc_final: 0.2427 (tpt) REVERT: A 86 PHE cc_start: 0.8680 (OUTLIER) cc_final: 0.7008 (t80) REVERT: A 338 ILE cc_start: 0.7851 (OUTLIER) cc_final: 0.7229 (mt) REVERT: A 413 GLU cc_start: 0.7332 (tp30) cc_final: 0.6310 (tm-30) REVERT: A 445 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7231 (mp0) REVERT: B 86 PHE cc_start: 0.8762 (OUTLIER) cc_final: 0.7422 (t80) REVERT: B 123 GLN cc_start: 0.7915 (mp10) cc_final: 0.7627 (mp-120) REVERT: B 151 MET cc_start: 0.8614 (mmm) cc_final: 0.8126 (mmm) REVERT: B 227 ARG cc_start: 0.7008 (mtp-110) cc_final: 0.6568 (ttp-110) REVERT: B 231 TRP cc_start: 0.8538 (OUTLIER) cc_final: 0.7973 (t-100) REVERT: B 338 ILE cc_start: 0.7966 (OUTLIER) cc_final: 0.7332 (mt) REVERT: B 546 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.6839 (tpt170) outliers start: 11 outliers final: 3 residues processed: 115 average time/residue: 0.4357 time to fit residues: 53.9417 Evaluate side-chains 119 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU 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 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 Chi-restraints excluded: chain B residue 546 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 70 optimal weight: 8.9990 chunk 4 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 15 optimal weight: 0.3980 chunk 34 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.146801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.106761 restraints weight = 7820.177| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.39 r_work: 0.3149 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8762 Z= 0.134 Angle : 0.561 7.167 11920 Z= 0.279 Chirality : 0.042 0.192 1390 Planarity : 0.006 0.060 1384 Dihedral : 10.496 89.343 1836 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.32 (0.27), residues: 1014 helix: 1.91 (0.18), residues: 792 sheet: None (None), residues: 0 loop : 0.32 (0.46), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 227 TYR 0.006 0.001 TYR B 332 PHE 0.019 0.001 PHE A 352 TRP 0.025 0.002 TRP A 418 HIS 0.018 0.003 HIS A 457 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 8762) covalent geometry : angle 0.56118 (11920) hydrogen bonds : bond 0.03925 ( 556) hydrogen bonds : angle 4.02147 ( 1626) ********************** 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 122 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.2766 (tpt) cc_final: 0.2440 (tpt) REVERT: A 86 PHE cc_start: 0.8702 (OUTLIER) cc_final: 0.6910 (t80) REVERT: A 227 ARG cc_start: 0.7292 (mtp-110) cc_final: 0.6793 (ttp-110) REVERT: A 338 ILE cc_start: 0.7876 (OUTLIER) cc_final: 0.7329 (mt) REVERT: A 413 GLU cc_start: 0.7341 (tp30) cc_final: 0.6333 (tm-30) REVERT: A 445 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7260 (mp0) REVERT: B 86 PHE cc_start: 0.8782 (OUTLIER) cc_final: 0.7454 (t80) REVERT: B 123 GLN cc_start: 0.7923 (mp10) cc_final: 0.7665 (mp-120) REVERT: B 151 MET cc_start: 0.8620 (mmm) cc_final: 0.8126 (mmm) REVERT: B 227 ARG cc_start: 0.6981 (mtp-110) cc_final: 0.6589 (ttp-110) REVERT: B 231 TRP cc_start: 0.8544 (OUTLIER) cc_final: 0.7948 (t-100) REVERT: B 338 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7340 (mt) REVERT: B 546 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.6877 (tpt170) outliers start: 12 outliers final: 4 residues processed: 118 average time/residue: 0.4223 time to fit residues: 53.5096 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 : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU 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 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 Chi-restraints excluded: chain B residue 546 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 41 optimal weight: 0.4980 chunk 44 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 94 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3786 r_free = 0.3786 target = 0.147661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.107748 restraints weight = 7772.731| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.39 r_work: 0.3168 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8762 Z= 0.121 Angle : 0.543 6.987 11920 Z= 0.270 Chirality : 0.041 0.188 1390 Planarity : 0.006 0.059 1384 Dihedral : 10.411 89.489 1836 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 1.63 % Allowed : 9.88 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.39 (0.27), residues: 1014 helix: 1.96 (0.18), residues: 792 sheet: None (None), residues: 0 loop : 0.34 (0.46), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 227 TYR 0.006 0.001 TYR B 332 PHE 0.018 0.001 PHE A 352 TRP 0.024 0.002 TRP A 418 HIS 0.018 0.003 HIS A 457 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 8762) covalent geometry : angle 0.54279 (11920) hydrogen bonds : bond 0.03685 ( 556) hydrogen bonds : angle 3.94880 ( 1626) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3608.58 seconds wall clock time: 61 minutes 54.17 seconds (3714.17 seconds total)