Starting phenix.real_space_refine on Sat Aug 23 15:53:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fyf_29572/08_2025/8fyf_29572.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fyf_29572/08_2025/8fyf_29572.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fyf_29572/08_2025/8fyf_29572.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fyf_29572/08_2025/8fyf_29572.map" model { file = "/net/cci-nas-00/data/ceres_data/8fyf_29572/08_2025/8fyf_29572.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fyf_29572/08_2025/8fyf_29572.cif" } resolution = 3.4 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= 0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians S 38 5.16 5 C 4244 2.51 5 N 1086 2.21 5 O 1080 1.98 5 H 6754 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 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: 13202 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 6163 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 16, 'TRANS': 370} Chain breaks: 1 Chain: "B" Number of atoms: 6163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 6163 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 16, 'TRANS': 370} Chain breaks: 1 Chain: "C" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 438 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 1, 'TRANS': 26} Chain: "D" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 438 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 1, 'TRANS': 26} Time building chain proxies: 2.88, per 1000 atoms: 0.22 Number of scatterers: 13202 At special positions: 0 Unit cell: (105.25, 73.254, 82.516, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 O 1080 8.00 N 1086 7.00 C 4244 6.00 H 6754 1.00 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: 1.00 Conformation dependent library (CDL) restraints added in 465.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1576 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 4 sheets defined 89.4% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 33 through 50 Processing helix chain 'A' and resid 51 through 57 removed outlier: 4.354A pdb=" N VAL A 55 " --> pdb=" O MET A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 102 removed outlier: 5.521A pdb=" N ARG A 72 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU A 73 " --> pdb=" O SER A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 121 Processing helix chain 'A' and resid 122 through 133 Processing helix chain 'A' and resid 136 through 164 removed outlier: 4.447A pdb=" N ILE A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 169 through 175 Processing helix chain 'A' and resid 177 through 190 removed outlier: 3.882A pdb=" N ARG A 183 " --> pdb=" O ALA A 179 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU A 186 " --> pdb=" O ARG A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 274 Processing helix chain 'A' and resid 274 through 284 removed outlier: 3.977A pdb=" N LEU A 278 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ASP A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 294 Processing helix chain 'A' and resid 298 through 305 Processing helix chain 'A' and resid 306 through 332 removed outlier: 3.701A pdb=" N PHE A 310 " --> pdb=" O THR A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 353 Processing helix chain 'A' and resid 354 through 364 Processing helix chain 'A' and resid 368 through 399 removed outlier: 3.881A pdb=" N GLU A 372 " --> pdb=" O GLN A 368 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLN A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 405 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 415 through 440 removed outlier: 4.910A pdb=" N TYR A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Proline residue: A 427 - end of helix removed outlier: 3.566A pdb=" N THR A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N CYS A 438 " --> pdb=" O PHE A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 461 Proline residue: A 456 - end of helix Processing helix chain 'A' and resid 461 through 474 Processing helix chain 'B' and resid 33 through 50 Processing helix chain 'B' and resid 51 through 57 removed outlier: 4.354A pdb=" N VAL B 55 " --> pdb=" O MET B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 102 removed outlier: 5.521A pdb=" N ARG B 72 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU B 73 " --> pdb=" O SER B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 121 removed outlier: 3.500A pdb=" N LEU B 111 " --> pdb=" O ASP B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 133 Processing helix chain 'B' and resid 136 through 164 removed outlier: 4.447A pdb=" N ILE B 140 " --> pdb=" O VAL B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 168 Processing helix chain 'B' and resid 169 through 175 Processing helix chain 'B' and resid 177 through 190 removed outlier: 3.886A pdb=" N ARG B 183 " --> pdb=" O ALA B 179 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU B 186 " --> pdb=" O ARG B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 274 Processing helix chain 'B' and resid 274 through 284 removed outlier: 3.977A pdb=" N LEU B 278 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ASP B 279 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE B 280 " --> pdb=" O LEU B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 294 Processing helix chain 'B' and resid 298 through 305 Processing helix chain 'B' and resid 306 through 332 removed outlier: 3.699A pdb=" N PHE B 310 " --> pdb=" O THR B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 353 Processing helix chain 'B' and resid 354 through 364 Processing helix chain 'B' and resid 368 through 399 removed outlier: 3.856A pdb=" N GLU B 372 " --> pdb=" O GLN B 368 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE B 389 " --> pdb=" O LEU B 385 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLN B 390 " --> pdb=" O ALA B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 405 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 415 through 440 removed outlier: 4.911A pdb=" N TYR B 426 " --> pdb=" O LYS B 422 " (cutoff:3.500A) Proline residue: B 427 - end of helix removed outlier: 3.567A pdb=" N THR B 437 " --> pdb=" O ALA B 433 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N CYS B 438 " --> pdb=" O PHE B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 461 Proline residue: B 456 - end of helix Processing helix chain 'B' and resid 461 through 474 Processing helix chain 'C' and resid 384 through 410 Processing helix chain 'D' and resid 384 through 410 Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 32 Processing sheet with id=AA2, first strand: chain 'A' and resid 255 through 256 removed outlier: 4.266A pdb=" N ALA A 337 " --> pdb=" O LEU A 256 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 31 through 32 Processing sheet with id=AA4, first strand: chain 'B' and resid 255 through 256 removed outlier: 4.287A pdb=" N ALA B 337 " --> pdb=" O LEU B 256 " (cutoff:3.500A) 523 hydrogen bonds defined for protein. 1545 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: 3.17 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6736 1.03 - 1.23: 20 1.23 - 1.42: 2680 1.42 - 1.61: 3852 1.61 - 1.81: 58 Bond restraints: 13346 Sorted by residual: bond pdb=" C THR B 306 " pdb=" N GLY B 307 " ideal model delta sigma weight residual 1.340 1.328 0.012 6.60e-03 2.30e+04 3.27e+00 bond pdb=" C THR A 306 " pdb=" N GLY A 307 " ideal model delta sigma weight residual 1.340 1.328 0.012 6.60e-03 2.30e+04 3.12e+00 bond pdb=" N LEU C 383 " pdb=" CA LEU C 383 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.08e+00 bond pdb=" N LEU D 383 " pdb=" CA LEU D 383 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.05e+00 bond pdb=" N ILE A 30 " pdb=" CA ILE A 30 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.68e+00 ... (remaining 13341 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 23336 1.34 - 2.68: 794 2.68 - 4.02: 58 4.02 - 5.36: 12 5.36 - 6.71: 2 Bond angle restraints: 24202 Sorted by residual: angle pdb=" N GLU A 403 " pdb=" CA GLU A 403 " pdb=" C GLU A 403 " ideal model delta sigma weight residual 114.56 111.34 3.22 1.27e+00 6.20e-01 6.45e+00 angle pdb=" N GLU B 403 " pdb=" CA GLU B 403 " pdb=" C GLU B 403 " ideal model delta sigma weight residual 114.56 111.36 3.20 1.27e+00 6.20e-01 6.35e+00 angle pdb=" C ILE A 60 " pdb=" N SER A 61 " pdb=" CA SER A 61 " ideal model delta sigma weight residual 122.00 119.39 2.61 1.08e+00 8.57e-01 5.86e+00 angle pdb=" N SER B 61 " pdb=" CA SER B 61 " pdb=" C SER B 61 " ideal model delta sigma weight residual 108.55 112.86 -4.31 1.79e+00 3.12e-01 5.81e+00 angle pdb=" C ILE B 60 " pdb=" N SER B 61 " pdb=" CA SER B 61 " ideal model delta sigma weight residual 122.00 119.43 2.57 1.08e+00 8.57e-01 5.66e+00 ... (remaining 24197 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 5611 17.62 - 35.23: 459 35.23 - 52.85: 127 52.85 - 70.47: 43 70.47 - 88.09: 8 Dihedral angle restraints: 6248 sinusoidal: 3352 harmonic: 2896 Sorted by residual: dihedral pdb=" CA GLU A 59 " pdb=" C GLU A 59 " pdb=" N ILE A 60 " pdb=" CA ILE A 60 " ideal model delta harmonic sigma weight residual -180.00 -159.95 -20.05 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA GLU B 59 " pdb=" C GLU B 59 " pdb=" N ILE B 60 " pdb=" CA ILE B 60 " ideal model delta harmonic sigma weight residual 180.00 -159.96 -20.04 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA LEU A 276 " pdb=" C LEU A 276 " pdb=" N ILE A 277 " pdb=" CA ILE A 277 " ideal model delta harmonic sigma weight residual 180.00 160.05 19.95 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 6245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 716 0.028 - 0.055: 235 0.055 - 0.083: 109 0.083 - 0.111: 36 0.111 - 0.138: 10 Chirality restraints: 1106 Sorted by residual: chirality pdb=" CA ILE A 30 " pdb=" N ILE A 30 " pdb=" C ILE A 30 " pdb=" CB ILE A 30 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.79e-01 chirality pdb=" CA ILE B 30 " pdb=" N ILE B 30 " pdb=" C ILE B 30 " pdb=" CB ILE B 30 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.75e-01 chirality pdb=" CA VAL B 136 " pdb=" N VAL B 136 " pdb=" C VAL B 136 " pdb=" CB VAL B 136 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.88e-01 ... (remaining 1103 not shown) Planarity restraints: 1888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 254 " -0.023 5.00e-02 4.00e+02 3.41e-02 1.87e+00 pdb=" N PRO B 255 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 255 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 255 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 287 " -0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO B 288 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 288 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 288 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 287 " -0.022 5.00e-02 4.00e+02 3.37e-02 1.82e+00 pdb=" N PRO A 288 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 288 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 288 " -0.019 5.00e-02 4.00e+02 ... (remaining 1885 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 203 2.08 - 2.71: 21938 2.71 - 3.34: 39930 3.34 - 3.97: 47602 3.97 - 4.60: 76240 Nonbonded interactions: 185913 Sorted by model distance: nonbonded pdb=" OE1 GLU A 259 " pdb=" H GLU A 259 " model vdw 1.451 2.450 nonbonded pdb=" OE1 GLU B 259 " pdb=" H GLU B 259 " model vdw 1.452 2.450 nonbonded pdb=" OE1 GLN A 171 " pdb=" H GLN A 171 " model vdw 1.633 2.450 nonbonded pdb=" OE1 GLN B 171 " pdb=" H GLN B 171 " model vdw 1.637 2.450 nonbonded pdb=" HE2 HIS A 95 " pdb=" OD1 ASN A 113 " model vdw 1.666 2.450 ... (remaining 185908 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 1.600 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: 0.080 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.670 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 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 : 0.003 0.033 6592 Z= 0.152 Angle : 0.582 6.706 8974 Z= 0.331 Chirality : 0.036 0.138 1106 Planarity : 0.004 0.034 1098 Dihedral : 14.089 88.087 2318 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.14 % Allowed : 10.34 % Favored : 89.51 % 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: 2.89 (0.30), residues: 818 helix: 2.32 (0.20), residues: 686 sheet: None (None), residues: 0 loop : -0.24 (0.63), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 335 TYR 0.008 0.001 TYR A 313 PHE 0.011 0.001 PHE B 314 TRP 0.012 0.002 TRP A 324 HIS 0.003 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 6592) covalent geometry : angle 0.58153 ( 8974) hydrogen bonds : bond 0.11443 ( 523) hydrogen bonds : angle 4.80284 ( 1545) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 0.423 Fit side-chains REVERT: B 426 TYR cc_start: 0.9087 (OUTLIER) cc_final: 0.7217 (t80) outliers start: 1 outliers final: 0 residues processed: 75 average time/residue: 0.1887 time to fit residues: 19.4657 Evaluate side-chains 72 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 426 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.123565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.093360 restraints weight = 32851.019| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.41 r_work: 0.2935 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.0632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 6592 Z= 0.205 Angle : 0.580 5.135 8974 Z= 0.316 Chirality : 0.038 0.113 1106 Planarity : 0.005 0.034 1098 Dihedral : 4.992 49.232 892 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.86 % Allowed : 10.78 % Favored : 88.36 % 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: 2.66 (0.30), residues: 818 helix: 2.23 (0.19), residues: 690 sheet: None (None), residues: 0 loop : -0.95 (0.63), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 309 TYR 0.010 0.001 TYR A 160 PHE 0.011 0.002 PHE B 99 TRP 0.010 0.001 TRP B 324 HIS 0.004 0.001 HIS A 449 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 6592) covalent geometry : angle 0.58022 ( 8974) hydrogen bonds : bond 0.05570 ( 523) hydrogen bonds : angle 4.49462 ( 1545) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.391 Fit side-chains REVERT: A 65 GLN cc_start: 0.3441 (OUTLIER) cc_final: 0.2710 (tm-30) REVERT: A 284 ASN cc_start: 0.8251 (t0) cc_final: 0.8030 (m-40) REVERT: A 293 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7163 (mp0) REVERT: A 426 TYR cc_start: 0.9151 (OUTLIER) cc_final: 0.7370 (t80) REVERT: B 65 GLN cc_start: 0.3433 (OUTLIER) cc_final: 0.2701 (tm-30) REVERT: B 284 ASN cc_start: 0.8273 (t0) cc_final: 0.8049 (m-40) REVERT: B 293 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7148 (mp0) REVERT: B 426 TYR cc_start: 0.9134 (OUTLIER) cc_final: 0.7259 (t80) outliers start: 6 outliers final: 0 residues processed: 82 average time/residue: 0.1708 time to fit residues: 19.6059 Evaluate side-chains 72 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 426 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 22 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 3 optimal weight: 0.0770 overall best weight: 1.9544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.124351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.093088 restraints weight = 32944.159| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.48 r_work: 0.2936 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.0800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6592 Z= 0.164 Angle : 0.550 5.036 8974 Z= 0.294 Chirality : 0.037 0.110 1106 Planarity : 0.004 0.032 1098 Dihedral : 4.939 49.933 892 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.15 % Allowed : 11.35 % Favored : 87.50 % 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: 2.82 (0.30), residues: 818 helix: 2.31 (0.19), residues: 690 sheet: None (None), residues: 0 loop : -0.70 (0.64), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 77 TYR 0.009 0.001 TYR B 313 PHE 0.010 0.001 PHE B 264 TRP 0.011 0.001 TRP B 324 HIS 0.004 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 6592) covalent geometry : angle 0.55018 ( 8974) hydrogen bonds : bond 0.05221 ( 523) hydrogen bonds : angle 4.30459 ( 1545) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.354 Fit side-chains REVERT: A 65 GLN cc_start: 0.3443 (OUTLIER) cc_final: 0.2723 (tm-30) REVERT: A 284 ASN cc_start: 0.8260 (t0) cc_final: 0.8022 (m-40) REVERT: A 293 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7194 (mp0) REVERT: A 426 TYR cc_start: 0.9165 (OUTLIER) cc_final: 0.7284 (t80) REVERT: B 65 GLN cc_start: 0.3444 (OUTLIER) cc_final: 0.2710 (tm-30) REVERT: B 284 ASN cc_start: 0.8278 (t0) cc_final: 0.8033 (m-40) REVERT: B 293 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7189 (mp0) REVERT: B 426 TYR cc_start: 0.9156 (OUTLIER) cc_final: 0.7303 (t80) outliers start: 8 outliers final: 2 residues processed: 82 average time/residue: 0.1712 time to fit residues: 19.5554 Evaluate side-chains 82 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 426 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 18 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.123413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.093519 restraints weight = 32869.422| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.38 r_work: 0.2926 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 6592 Z= 0.211 Angle : 0.568 5.072 8974 Z= 0.307 Chirality : 0.038 0.113 1106 Planarity : 0.004 0.033 1098 Dihedral : 5.009 50.023 892 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.58 % Allowed : 12.36 % Favored : 86.06 % 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: 2.62 (0.30), residues: 818 helix: 2.18 (0.19), residues: 690 sheet: None (None), residues: 0 loop : -0.73 (0.64), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 442 TYR 0.010 0.001 TYR A 313 PHE 0.012 0.002 PHE A 264 TRP 0.010 0.001 TRP B 324 HIS 0.005 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00473 ( 6592) covalent geometry : angle 0.56837 ( 8974) hydrogen bonds : bond 0.05273 ( 523) hydrogen bonds : angle 4.32664 ( 1545) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.372 Fit side-chains REVERT: A 65 GLN cc_start: 0.3454 (OUTLIER) cc_final: 0.2558 (tm-30) REVERT: A 284 ASN cc_start: 0.8242 (t0) cc_final: 0.7971 (m-40) REVERT: A 293 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7090 (mp0) REVERT: B 65 GLN cc_start: 0.3403 (OUTLIER) cc_final: 0.2559 (tm-30) REVERT: B 284 ASN cc_start: 0.8259 (t0) cc_final: 0.7987 (m-40) REVERT: B 293 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7101 (mp0) outliers start: 11 outliers final: 7 residues processed: 90 average time/residue: 0.1660 time to fit residues: 21.0662 Evaluate side-chains 86 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain D residue 386 ILE Chi-restraints excluded: chain D residue 395 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 1 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 54 optimal weight: 0.5980 chunk 47 optimal weight: 0.4980 chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 HIS B 177 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.125040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.095467 restraints weight = 32623.915| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.39 r_work: 0.2975 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6592 Z= 0.134 Angle : 0.528 4.970 8974 Z= 0.279 Chirality : 0.036 0.110 1106 Planarity : 0.004 0.032 1098 Dihedral : 4.850 50.870 892 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.16 % Allowed : 11.93 % Favored : 85.92 % 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: 3.02 (0.30), residues: 818 helix: 2.46 (0.19), residues: 690 sheet: None (None), residues: 0 loop : -0.71 (0.65), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 260 TYR 0.009 0.001 TYR B 313 PHE 0.009 0.001 PHE A 99 TRP 0.011 0.001 TRP B 324 HIS 0.003 0.001 HIS B 327 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 6592) covalent geometry : angle 0.52752 ( 8974) hydrogen bonds : bond 0.04827 ( 523) hydrogen bonds : angle 4.13308 ( 1545) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 GLN cc_start: 0.3438 (OUTLIER) cc_final: 0.2745 (tm-30) REVERT: A 284 ASN cc_start: 0.8200 (t0) cc_final: 0.7961 (m-40) REVERT: A 293 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7107 (mp0) REVERT: A 426 TYR cc_start: 0.9166 (OUTLIER) cc_final: 0.7285 (t80) REVERT: B 65 GLN cc_start: 0.3436 (OUTLIER) cc_final: 0.2734 (tm-30) REVERT: B 284 ASN cc_start: 0.8211 (t0) cc_final: 0.7972 (m-40) REVERT: B 293 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7107 (mp0) REVERT: B 426 TYR cc_start: 0.9151 (OUTLIER) cc_final: 0.7201 (t80) outliers start: 15 outliers final: 8 residues processed: 90 average time/residue: 0.1969 time to fit residues: 23.7151 Evaluate side-chains 88 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 177 HIS Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 309 ARG Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 177 HIS Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain D residue 386 ILE Chi-restraints excluded: chain D residue 395 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 HIS B 177 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.125313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.093949 restraints weight = 32565.387| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.48 r_work: 0.2935 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6592 Z= 0.157 Angle : 0.532 4.946 8974 Z= 0.286 Chirality : 0.036 0.111 1106 Planarity : 0.004 0.033 1098 Dihedral : 4.867 50.773 892 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.16 % Allowed : 11.78 % Favored : 86.06 % 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: 3.06 (0.30), residues: 818 helix: 2.50 (0.19), residues: 690 sheet: None (None), residues: 0 loop : -0.79 (0.64), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 178 TYR 0.009 0.001 TYR A 313 PHE 0.010 0.001 PHE A 99 TRP 0.009 0.001 TRP B 324 HIS 0.024 0.002 HIS A 177 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 6592) covalent geometry : angle 0.53246 ( 8974) hydrogen bonds : bond 0.04810 ( 523) hydrogen bonds : angle 4.14675 ( 1545) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 GLN cc_start: 0.3449 (OUTLIER) cc_final: 0.2747 (tm-30) REVERT: A 284 ASN cc_start: 0.8194 (t0) cc_final: 0.7942 (m-40) REVERT: A 293 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7084 (mp0) REVERT: A 426 TYR cc_start: 0.9186 (OUTLIER) cc_final: 0.7314 (t80) REVERT: B 65 GLN cc_start: 0.3420 (OUTLIER) cc_final: 0.2722 (tm-30) REVERT: B 284 ASN cc_start: 0.8214 (t0) cc_final: 0.7958 (m-40) REVERT: B 293 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7080 (mp0) REVERT: B 426 TYR cc_start: 0.9167 (OUTLIER) cc_final: 0.7213 (t80) outliers start: 15 outliers final: 8 residues processed: 87 average time/residue: 0.2028 time to fit residues: 23.4229 Evaluate side-chains 88 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 177 HIS Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 309 ARG Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 177 HIS Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain D residue 386 ILE Chi-restraints excluded: chain D residue 395 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 14 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.124423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.094745 restraints weight = 32438.582| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.40 r_work: 0.2953 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6592 Z= 0.134 Angle : 0.518 4.900 8974 Z= 0.277 Chirality : 0.036 0.111 1106 Planarity : 0.004 0.033 1098 Dihedral : 4.769 51.002 892 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.87 % Allowed : 11.93 % Favored : 86.21 % 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: 3.21 (0.30), residues: 818 helix: 2.61 (0.19), residues: 690 sheet: None (None), residues: 0 loop : -0.76 (0.64), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 309 TYR 0.009 0.001 TYR A 313 PHE 0.009 0.001 PHE A 99 TRP 0.010 0.001 TRP B 324 HIS 0.003 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 6592) covalent geometry : angle 0.51848 ( 8974) hydrogen bonds : bond 0.04637 ( 523) hydrogen bonds : angle 4.02571 ( 1545) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 GLN cc_start: 0.3470 (OUTLIER) cc_final: 0.2768 (tm-30) REVERT: A 284 ASN cc_start: 0.8182 (t0) cc_final: 0.7929 (m-40) REVERT: A 293 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7080 (mp0) REVERT: A 426 TYR cc_start: 0.9140 (OUTLIER) cc_final: 0.7275 (t80) REVERT: B 65 GLN cc_start: 0.3424 (OUTLIER) cc_final: 0.2729 (tm-30) REVERT: B 284 ASN cc_start: 0.8196 (t0) cc_final: 0.7940 (m-40) REVERT: B 293 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7083 (mp0) REVERT: B 426 TYR cc_start: 0.9120 (OUTLIER) cc_final: 0.7141 (t80) outliers start: 13 outliers final: 7 residues processed: 85 average time/residue: 0.2007 time to fit residues: 22.6658 Evaluate side-chains 88 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 309 ARG Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain D residue 386 ILE Chi-restraints excluded: chain D residue 395 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.125137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.094100 restraints weight = 32359.838| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.48 r_work: 0.2981 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6592 Z= 0.132 Angle : 0.508 4.929 8974 Z= 0.270 Chirality : 0.036 0.112 1106 Planarity : 0.004 0.033 1098 Dihedral : 4.695 51.044 892 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.87 % Allowed : 11.64 % Favored : 86.49 % 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: 3.29 (0.30), residues: 818 helix: 2.67 (0.19), residues: 690 sheet: None (None), residues: 0 loop : -0.76 (0.65), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 260 TYR 0.008 0.001 TYR B 313 PHE 0.009 0.001 PHE A 99 TRP 0.010 0.001 TRP B 324 HIS 0.003 0.001 HIS A 177 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 6592) covalent geometry : angle 0.50848 ( 8974) hydrogen bonds : bond 0.04490 ( 523) hydrogen bonds : angle 3.98932 ( 1545) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.356 Fit side-chains REVERT: A 65 GLN cc_start: 0.3634 (OUTLIER) cc_final: 0.2871 (tm-30) REVERT: A 293 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7007 (mp0) REVERT: A 426 TYR cc_start: 0.9148 (OUTLIER) cc_final: 0.7275 (t80) REVERT: B 65 GLN cc_start: 0.3401 (OUTLIER) cc_final: 0.2658 (tm-30) REVERT: B 293 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7070 (mp0) REVERT: B 426 TYR cc_start: 0.9126 (OUTLIER) cc_final: 0.7127 (t80) outliers start: 13 outliers final: 5 residues processed: 87 average time/residue: 0.2025 time to fit residues: 23.5248 Evaluate side-chains 86 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain D residue 386 ILE Chi-restraints excluded: chain D residue 395 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 77 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 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 284 ASN B 284 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.126192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.096575 restraints weight = 32458.762| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.40 r_work: 0.2971 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6592 Z= 0.121 Angle : 0.504 5.327 8974 Z= 0.268 Chirality : 0.035 0.110 1106 Planarity : 0.004 0.033 1098 Dihedral : 4.625 51.217 892 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.16 % Allowed : 11.21 % Favored : 86.64 % 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: 3.41 (0.30), residues: 818 helix: 2.76 (0.19), residues: 690 sheet: None (None), residues: 0 loop : -0.79 (0.64), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 309 TYR 0.008 0.001 TYR B 313 PHE 0.009 0.001 PHE A 99 TRP 0.010 0.001 TRP A 324 HIS 0.003 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 6592) covalent geometry : angle 0.50444 ( 8974) hydrogen bonds : bond 0.04313 ( 523) hydrogen bonds : angle 3.88960 ( 1545) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.385 Fit side-chains REVERT: A 65 GLN cc_start: 0.3584 (OUTLIER) cc_final: 0.2848 (tm-30) REVERT: A 293 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.6999 (mp0) REVERT: A 426 TYR cc_start: 0.9138 (OUTLIER) cc_final: 0.7295 (t80) REVERT: B 65 GLN cc_start: 0.3585 (OUTLIER) cc_final: 0.2848 (tm-30) REVERT: B 293 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7009 (mp0) REVERT: B 426 TYR cc_start: 0.9113 (OUTLIER) cc_final: 0.7154 (t80) outliers start: 15 outliers final: 4 residues processed: 84 average time/residue: 0.1700 time to fit residues: 20.0526 Evaluate side-chains 85 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain D residue 386 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 59 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.125217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.095524 restraints weight = 32425.872| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.40 r_work: 0.2991 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6592 Z= 0.143 Angle : 0.513 5.221 8974 Z= 0.273 Chirality : 0.036 0.115 1106 Planarity : 0.004 0.034 1098 Dihedral : 4.621 50.950 892 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.29 % Allowed : 12.36 % Favored : 86.35 % 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: 3.31 (0.30), residues: 818 helix: 2.69 (0.19), residues: 690 sheet: None (None), residues: 0 loop : -0.78 (0.65), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 309 TYR 0.008 0.001 TYR B 313 PHE 0.010 0.001 PHE A 99 TRP 0.008 0.001 TRP B 324 HIS 0.003 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 6592) covalent geometry : angle 0.51314 ( 8974) hydrogen bonds : bond 0.04405 ( 523) hydrogen bonds : angle 3.91544 ( 1545) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.383 Fit side-chains REVERT: A 293 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7028 (mp0) REVERT: A 426 TYR cc_start: 0.9164 (OUTLIER) cc_final: 0.7280 (t80) REVERT: B 65 GLN cc_start: 0.3615 (OUTLIER) cc_final: 0.2740 (tm-30) REVERT: B 293 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7044 (mp0) REVERT: B 426 TYR cc_start: 0.9138 (OUTLIER) cc_final: 0.7128 (t80) outliers start: 9 outliers final: 4 residues processed: 82 average time/residue: 0.1713 time to fit residues: 19.6390 Evaluate side-chains 84 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain D residue 386 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 19 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.126394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.096831 restraints weight = 32255.515| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.40 r_work: 0.2969 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6592 Z= 0.119 Angle : 0.503 5.411 8974 Z= 0.264 Chirality : 0.035 0.111 1106 Planarity : 0.004 0.033 1098 Dihedral : 4.551 51.202 892 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.15 % Allowed : 12.64 % Favored : 86.21 % 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: 3.49 (0.30), residues: 818 helix: 2.83 (0.19), residues: 690 sheet: None (None), residues: 0 loop : -0.81 (0.64), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 260 TYR 0.009 0.001 TYR B 313 PHE 0.009 0.001 PHE B 448 TRP 0.010 0.001 TRP A 324 HIS 0.003 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 6592) covalent geometry : angle 0.50273 ( 8974) hydrogen bonds : bond 0.04216 ( 523) hydrogen bonds : angle 3.84780 ( 1545) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2834.32 seconds wall clock time: 49 minutes 3.92 seconds (2943.92 seconds total)