Starting phenix.real_space_refine on Sun May 11 20:35:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uvf_42618/05_2025/8uvf_42618.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uvf_42618/05_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_42618/05_2025/8uvf_42618.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uvf_42618/05_2025/8uvf_42618.map" model { file = "/net/cci-nas-00/data/ceres_data/8uvf_42618/05_2025/8uvf_42618.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uvf_42618/05_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-5687/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: 8.09, per 1000 atoms: 0.95 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: 2.34 Conformation dependent library (CDL) restraints added in 896.6 milliseconds 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: 0.81 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: 2.33 Time building geometry restraints manager: 2.70 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: 1.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 24.280 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:11.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.570 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.12006 ( 556) hydrogen bonds : angle 4.64040 ( 1626) covalent geometry : bond 0.00477 ( 8762) covalent geometry : angle 0.67533 (11920) *********************** 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 : 0.897 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 144 average time/residue: 1.3048 time to fit residues: 198.9539 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 : 0.803 ------------------------------------------------------------------------------- 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 = 51)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.114137 restraints weight = 7744.274| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.41 r_work: 0.3261 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- 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= 0.141 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 Details of bonding type rmsd hydrogen bonds : bond 0.04188 ( 556) hydrogen bonds : angle 4.02861 ( 1626) covalent geometry : bond 0.00321 ( 8762) covalent geometry : angle 0.61288 (11920) *********************** 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 : 0.954 Fit side-chains revert: symmetry clash REVERT: B 123 GLN cc_start: 0.7979 (mp10) cc_final: 0.7697 (mp-120) REVERT: B 510 MET cc_start: 0.9069 (mtp) cc_final: 0.8758 (mtp) outliers start: 7 outliers final: 3 residues processed: 128 average time/residue: 1.1845 time to fit residues: 162.1631 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 : 0.808 ------------------------------------------------------------------------------- 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: 0.9990 chunk 82 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 88 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 B 538 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.150341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.111073 restraints weight = 7885.392| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.37 r_work: 0.3224 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8762 Z= 0.159 Angle : 0.602 7.322 11920 Z= 0.298 Chirality : 0.044 0.153 1390 Planarity : 0.005 0.045 1384 Dihedral : 10.454 88.152 1836 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 0.93 % Allowed : 6.63 % Favored : 92.44 % 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: 2.22 (0.27), residues: 1014 helix: 1.80 (0.18), residues: 790 sheet: None (None), residues: 0 loop : 0.50 (0.47), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 418 HIS 0.019 0.004 HIS A 538 PHE 0.019 0.002 PHE A 352 TYR 0.009 0.001 TYR B 226 ARG 0.007 0.001 ARG A 227 Details of bonding type rmsd hydrogen bonds : bond 0.04437 ( 556) hydrogen bonds : angle 4.12886 ( 1626) covalent geometry : bond 0.00376 ( 8762) covalent geometry : angle 0.60202 (11920) *********************** 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 : 0.875 Fit side-chains revert: symmetry clash REVERT: B 86 PHE cc_start: 0.8863 (OUTLIER) cc_final: 0.7579 (t80) REVERT: B 123 GLN cc_start: 0.8015 (mp10) cc_final: 0.7739 (mp-120) REVERT: B 151 MET cc_start: 0.8668 (mmm) cc_final: 0.8164 (mmm) REVERT: B 445 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7240 (mp0) outliers start: 8 outliers final: 3 residues processed: 122 average time/residue: 1.0392 time to fit residues: 136.5101 Evaluate side-chains 115 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 110 time to evaluate : 0.826 ------------------------------------------------------------------------------- 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: 2.9990 chunk 18 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 5 optimal weight: 0.0980 chunk 91 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 36 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 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 = 0.3857 r_free = 0.3857 target = 0.152195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.113018 restraints weight = 7859.979| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.38 r_work: 0.3248 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1693 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= 0.122 Angle : 0.544 6.962 11920 Z= 0.271 Chirality : 0.041 0.167 1390 Planarity : 0.005 0.047 1384 Dihedral : 10.342 88.749 1836 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 1.28 % Allowed : 8.72 % Favored : 90.00 % 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: 2.37 (0.27), residues: 1014 helix: 1.95 (0.18), residues: 790 sheet: None (None), residues: 0 loop : 0.35 (0.46), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 418 HIS 0.017 0.003 HIS A 457 PHE 0.018 0.001 PHE A 352 TYR 0.006 0.001 TYR B 226 ARG 0.009 0.001 ARG B 227 Details of bonding type rmsd hydrogen bonds : bond 0.03727 ( 556) hydrogen bonds : angle 3.95078 ( 1626) covalent geometry : bond 0.00281 ( 8762) covalent geometry : angle 0.54403 (11920) *********************** 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 126 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 1.023 Fit side-chains revert: symmetry clash REVERT: A 86 PHE cc_start: 0.8742 (OUTLIER) cc_final: 0.7167 (t80) REVERT: A 445 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7217 (mp0) REVERT: B 86 PHE cc_start: 0.8794 (OUTLIER) cc_final: 0.7459 (t80) REVERT: B 123 GLN cc_start: 0.8023 (mp10) cc_final: 0.7764 (mp-120) REVERT: B 151 MET cc_start: 0.8689 (mmm) cc_final: 0.8211 (mmm) outliers start: 11 outliers final: 3 residues processed: 123 average time/residue: 1.0266 time to fit residues: 136.1296 Evaluate side-chains 118 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 112 time to evaluate : 0.879 ------------------------------------------------------------------------------- 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: 0.9980 chunk 13 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 34 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 B 538 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.146259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.106038 restraints weight = 7746.849| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.39 r_work: 0.3143 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1868 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 : 0.578 7.321 11920 Z= 0.289 Chirality : 0.043 0.168 1390 Planarity : 0.005 0.048 1384 Dihedral : 10.573 89.047 1836 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 1.63 % Allowed : 8.60 % Favored : 89.77 % 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: 1.86 (0.18), residues: 790 sheet: None (None), residues: 0 loop : 0.40 (0.46), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 418 HIS 0.020 0.004 HIS A 457 PHE 0.019 0.002 PHE A 352 TYR 0.008 0.001 TYR B 332 ARG 0.010 0.001 ARG B 227 Details of bonding type rmsd hydrogen bonds : bond 0.04265 ( 556) hydrogen bonds : angle 4.08632 ( 1626) covalent geometry : bond 0.00357 ( 8762) covalent geometry : angle 0.57811 (11920) *********************** 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 128 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.845 Fit side-chains revert: symmetry clash REVERT: A 86 PHE cc_start: 0.8751 (OUTLIER) cc_final: 0.7105 (t80) REVERT: A 231 TRP cc_start: 0.8693 (OUTLIER) cc_final: 0.8470 (t-100) REVERT: A 338 ILE cc_start: 0.7862 (OUTLIER) cc_final: 0.7226 (mt) REVERT: A 413 GLU cc_start: 0.7554 (mm-30) cc_final: 0.6447 (tm-30) REVERT: B 86 PHE cc_start: 0.8801 (OUTLIER) cc_final: 0.7367 (t80) REVERT: B 123 GLN cc_start: 0.7945 (mp10) cc_final: 0.7676 (mp-120) REVERT: B 151 MET cc_start: 0.8624 (mmm) cc_final: 0.8132 (mmm) REVERT: B 231 TRP cc_start: 0.8595 (OUTLIER) cc_final: 0.8021 (t-100) REVERT: B 385 ILE cc_start: 0.8586 (mm) cc_final: 0.8371 (mt) outliers start: 14 outliers final: 2 residues processed: 124 average time/residue: 1.0129 time to fit residues: 135.5798 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 : 0.843 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 73 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 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 A 538 HIS B 457 HIS B 538 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.147108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.106971 restraints weight = 7733.670| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.39 r_work: 0.3158 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1949 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= 0.133 Angle : 0.556 7.073 11920 Z= 0.277 Chirality : 0.042 0.177 1390 Planarity : 0.005 0.050 1384 Dihedral : 10.426 89.716 1836 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 1.28 % Allowed : 9.65 % Favored : 89.07 % 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: 2.32 (0.27), residues: 1014 helix: 1.90 (0.18), residues: 792 sheet: None (None), residues: 0 loop : 0.36 (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 0.018 0.001 PHE A 352 TYR 0.006 0.001 TYR B 332 ARG 0.011 0.001 ARG A 227 Details of bonding type rmsd hydrogen bonds : bond 0.03921 ( 556) hydrogen bonds : angle 3.99692 ( 1626) covalent geometry : bond 0.00314 ( 8762) covalent geometry : angle 0.55618 (11920) *********************** 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 123 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.934 Fit side-chains revert: symmetry clash REVERT: A 55 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7462 (mt-10) REVERT: A 86 PHE cc_start: 0.8701 (OUTLIER) cc_final: 0.7029 (t80) REVERT: A 231 TRP cc_start: 0.8679 (OUTLIER) cc_final: 0.8459 (t-100) REVERT: A 445 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7219 (mp0) REVERT: B 86 PHE cc_start: 0.8778 (OUTLIER) cc_final: 0.7449 (t80) REVERT: B 123 GLN cc_start: 0.7943 (mp10) cc_final: 0.7683 (mp-120) REVERT: B 151 MET cc_start: 0.8608 (mmm) cc_final: 0.8115 (mmm) REVERT: B 227 ARG cc_start: 0.7077 (mtp-110) cc_final: 0.6678 (ttp-110) REVERT: B 231 TRP cc_start: 0.8595 (OUTLIER) cc_final: 0.8085 (t-100) REVERT: B 338 ILE cc_start: 0.7955 (OUTLIER) cc_final: 0.7339 (mt) outliers start: 11 outliers final: 1 residues processed: 118 average time/residue: 1.0060 time to fit residues: 128.0576 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 : 0.829 ------------------------------------------------------------------------------- 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 231 TRP 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 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: 0.5980 chunk 97 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 72 optimal weight: 0.4980 chunk 24 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3783 r_free = 0.3783 target = 0.147327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.107249 restraints weight = 7758.661| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.39 r_work: 0.3160 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2000 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= 0.129 Angle : 0.548 7.027 11920 Z= 0.273 Chirality : 0.042 0.195 1390 Planarity : 0.005 0.050 1384 Dihedral : 10.297 89.584 1836 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.74 % Allowed : 9.19 % Favored : 89.07 % 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: 1.93 (0.18), residues: 792 sheet: None (None), residues: 0 loop : 0.35 (0.47), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 418 HIS 0.018 0.004 HIS A 457 PHE 0.019 0.001 PHE A 352 TYR 0.006 0.001 TYR B 332 ARG 0.012 0.001 ARG A 227 Details of bonding type rmsd hydrogen bonds : bond 0.03869 ( 556) hydrogen bonds : angle 3.98969 ( 1626) covalent geometry : bond 0.00300 ( 8762) covalent geometry : angle 0.54783 (11920) *********************** 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 127 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.837 Fit side-chains revert: symmetry clash REVERT: A 86 PHE cc_start: 0.8684 (OUTLIER) cc_final: 0.7014 (t80) REVERT: A 227 ARG cc_start: 0.7266 (mtp-110) cc_final: 0.6811 (ttp-110) REVERT: A 231 TRP cc_start: 0.8680 (OUTLIER) cc_final: 0.8450 (t-100) REVERT: A 338 ILE cc_start: 0.7834 (OUTLIER) cc_final: 0.7217 (mt) REVERT: A 445 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7232 (mp0) REVERT: B 86 PHE cc_start: 0.8763 (OUTLIER) cc_final: 0.7426 (t80) REVERT: B 123 GLN cc_start: 0.7920 (mp10) cc_final: 0.7634 (mp-120) REVERT: B 151 MET cc_start: 0.8600 (mmm) cc_final: 0.8108 (mmm) REVERT: B 231 TRP cc_start: 0.8569 (OUTLIER) cc_final: 0.8029 (t-100) REVERT: B 338 ILE cc_start: 0.7942 (OUTLIER) cc_final: 0.7326 (mt) REVERT: B 385 ILE cc_start: 0.8564 (mm) cc_final: 0.8343 (mt) outliers start: 15 outliers final: 3 residues processed: 122 average time/residue: 0.9871 time to fit residues: 129.8296 Evaluate side-chains 122 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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 231 TRP 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 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: 4.9990 chunk 41 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 72 optimal weight: 0.0980 chunk 59 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3791 r_free = 0.3791 target = 0.148128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.108014 restraints weight = 7932.750| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.40 r_work: 0.3166 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8762 Z= 0.120 Angle : 0.537 6.887 11920 Z= 0.268 Chirality : 0.041 0.189 1390 Planarity : 0.005 0.058 1384 Dihedral : 10.172 89.991 1836 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 1.51 % Allowed : 10.00 % 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 (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: 2.40 (0.27), residues: 1014 helix: 1.97 (0.18), residues: 792 sheet: None (None), residues: 0 loop : 0.33 (0.46), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 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 0.011 0.000 ARG B 227 Details of bonding type rmsd hydrogen bonds : bond 0.03704 ( 556) hydrogen bonds : angle 3.92970 ( 1626) covalent geometry : bond 0.00275 ( 8762) covalent geometry : angle 0.53708 (11920) *********************** 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: 13 poor density : 113 time to evaluate : 0.936 Fit side-chains revert: symmetry clash REVERT: A 86 PHE cc_start: 0.8664 (OUTLIER) cc_final: 0.6994 (t80) REVERT: A 445 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7229 (mp0) REVERT: B 86 PHE cc_start: 0.8767 (OUTLIER) cc_final: 0.7271 (t80) REVERT: B 123 GLN cc_start: 0.7919 (mp10) cc_final: 0.7664 (mp-120) REVERT: B 227 ARG cc_start: 0.7054 (mtp-110) cc_final: 0.6632 (ttp-110) REVERT: B 231 TRP cc_start: 0.8576 (OUTLIER) cc_final: 0.8040 (t-100) outliers start: 13 outliers final: 3 residues processed: 122 average time/residue: 0.9770 time to fit residues: 129.2888 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 : 0.918 ------------------------------------------------------------------------------- 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 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 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: 0.9990 chunk 33 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 101 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3777 r_free = 0.3777 target = 0.146877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.106678 restraints weight = 7845.037| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.39 r_work: 0.3150 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8762 Z= 0.140 Angle : 0.566 7.151 11920 Z= 0.282 Chirality : 0.043 0.194 1390 Planarity : 0.006 0.060 1384 Dihedral : 10.305 89.620 1836 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.28 % Allowed : 10.58 % 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: 2.30 (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 0.002 PHE A 352 TYR 0.007 0.001 TYR B 332 ARG 0.014 0.001 ARG A 227 Details of bonding type rmsd hydrogen bonds : bond 0.04030 ( 556) hydrogen bonds : angle 4.01650 ( 1626) covalent geometry : bond 0.00331 ( 8762) covalent geometry : angle 0.56559 (11920) *********************** 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 125 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.951 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.2801 (tpt) cc_final: 0.2480 (tpt) REVERT: A 55 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7663 (mt-10) REVERT: A 86 PHE cc_start: 0.8698 (OUTLIER) cc_final: 0.6927 (t80) REVERT: A 227 ARG cc_start: 0.7300 (mtp-110) cc_final: 0.6812 (ttp-110) REVERT: A 338 ILE cc_start: 0.7838 (OUTLIER) cc_final: 0.7216 (mt) REVERT: A 445 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7242 (mp0) REVERT: B 86 PHE cc_start: 0.8769 (OUTLIER) cc_final: 0.7303 (t80) REVERT: B 123 GLN cc_start: 0.7918 (mp10) cc_final: 0.7652 (mp-120) REVERT: B 151 MET cc_start: 0.8614 (mmm) cc_final: 0.8117 (mmm) REVERT: B 227 ARG cc_start: 0.7050 (mtp-110) cc_final: 0.6612 (ttp-110) REVERT: B 231 TRP cc_start: 0.8565 (OUTLIER) cc_final: 0.8033 (t-100) REVERT: B 338 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7337 (mt) REVERT: B 385 ILE cc_start: 0.8566 (mm) cc_final: 0.8350 (mt) outliers start: 11 outliers final: 2 residues processed: 120 average time/residue: 1.0815 time to fit residues: 140.1360 Evaluate side-chains 120 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.970 ------------------------------------------------------------------------------- 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 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 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: 0.8980 chunk 75 optimal weight: 0.4980 chunk 70 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 96 optimal weight: 0.0040 chunk 15 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- 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 = 0.3788 r_free = 0.3788 target = 0.147936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.107915 restraints weight = 7802.315| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.39 r_work: 0.3167 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2096 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= 0.120 Angle : 0.542 6.955 11920 Z= 0.270 Chirality : 0.041 0.188 1390 Planarity : 0.005 0.055 1384 Dihedral : 10.236 89.728 1836 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 1.16 % Allowed : 10.70 % 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: 2.36 (0.27), residues: 1014 helix: 1.96 (0.18), residues: 792 sheet: None (None), residues: 0 loop : 0.26 (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 0.005 0.001 TYR B 332 ARG 0.014 0.001 ARG A 227 Details of bonding type rmsd hydrogen bonds : bond 0.03716 ( 556) hydrogen bonds : angle 3.94264 ( 1626) covalent geometry : bond 0.00275 ( 8762) covalent geometry : angle 0.54237 (11920) ********************** 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: 10 poor density : 114 time to evaluate : 0.806 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.2785 (tpt) cc_final: 0.2460 (tpt) REVERT: A 55 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7708 (mt-10) REVERT: A 86 PHE cc_start: 0.8656 (OUTLIER) cc_final: 0.6995 (t80) REVERT: A 227 ARG cc_start: 0.7247 (mtp-110) cc_final: 0.6762 (ttp-110) REVERT: A 338 ILE cc_start: 0.7841 (OUTLIER) cc_final: 0.7214 (mt) REVERT: A 445 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7230 (mp0) REVERT: B 86 PHE cc_start: 0.8770 (OUTLIER) cc_final: 0.7274 (t80) REVERT: B 123 GLN cc_start: 0.7899 (mp10) cc_final: 0.7635 (mp-120) REVERT: B 151 MET cc_start: 0.8620 (mmm) cc_final: 0.8140 (mmm) REVERT: B 227 ARG cc_start: 0.6961 (mtp-110) cc_final: 0.6620 (ttp-110) REVERT: B 231 TRP cc_start: 0.8559 (OUTLIER) cc_final: 0.8014 (t-100) REVERT: B 330 GLU cc_start: 0.7442 (tm-30) cc_final: 0.7223 (tm-30) REVERT: B 338 ILE cc_start: 0.7978 (OUTLIER) cc_final: 0.7329 (mt) REVERT: B 385 ILE cc_start: 0.8572 (mm) cc_final: 0.8350 (mt) outliers start: 10 outliers final: 1 residues processed: 120 average time/residue: 1.0219 time to fit residues: 132.4416 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 : 0.927 ------------------------------------------------------------------------------- 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 445 GLU 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: 2.9990 chunk 13 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 100 optimal weight: 0.5980 chunk 5 optimal weight: 0.4980 chunk 68 optimal weight: 1.9990 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 = 0.3790 r_free = 0.3790 target = 0.148099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.107976 restraints weight = 7867.813| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.40 r_work: 0.3169 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: 0.8442 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8762 Z= 0.121 Angle : 0.542 6.927 11920 Z= 0.270 Chirality : 0.041 0.194 1390 Planarity : 0.006 0.055 1384 Dihedral : 10.236 89.224 1836 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.30 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 (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: 2.35 (0.27), residues: 1014 helix: 1.96 (0.18), residues: 792 sheet: None (None), residues: 0 loop : 0.22 (0.46), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 418 HIS 0.019 0.003 HIS A 457 PHE 0.018 0.001 PHE A 352 TYR 0.005 0.001 TYR B 332 ARG 0.013 0.001 ARG A 227 Details of bonding type rmsd hydrogen bonds : bond 0.03728 ( 556) hydrogen bonds : angle 3.94411 ( 1626) covalent geometry : bond 0.00277 ( 8762) covalent geometry : angle 0.54232 (11920) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7707.87 seconds wall clock time: 133 minutes 0.55 seconds (7980.55 seconds total)