Starting phenix.real_space_refine on Wed Feb 4 09:21:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jxg_61862/02_2026/9jxg_61862.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jxg_61862/02_2026/9jxg_61862.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jxg_61862/02_2026/9jxg_61862.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jxg_61862/02_2026/9jxg_61862.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jxg_61862/02_2026/9jxg_61862.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jxg_61862/02_2026/9jxg_61862.map" } resolution = 3.75 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= 0.004 sd= 0.062 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: 4 Type Number sf(0) Gaussians S 38 5.16 5 C 6384 2.51 5 N 1596 2.21 5 O 1652 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9670 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 4835 Classifications: {'peptide': 580} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 561} Chain breaks: 3 Restraints were copied for chains: B Time building chain proxies: 3.25, per 1000 atoms: 0.34 Number of scatterers: 9670 At special positions: 0 Unit cell: (114.995, 125.545, 96.005, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 38 16.00 O 1652 8.00 N 1596 7.00 C 6384 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 352.5 milliseconds 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2224 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 0 sheets defined 79.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 23 through 36 removed outlier: 3.651A pdb=" N GLN A 35 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 99 Processing helix chain 'A' and resid 116 through 118 No H-bonds generated for 'chain 'A' and resid 116 through 118' Processing helix chain 'A' and resid 119 through 168 removed outlier: 3.787A pdb=" N LEU A 167 " --> pdb=" O HIS A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 181 Processing helix chain 'A' and resid 183 through 188 removed outlier: 3.929A pdb=" N CYS A 188 " --> pdb=" O PRO A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 206 removed outlier: 3.804A pdb=" N GLN A 193 " --> pdb=" O LYS A 189 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU A 205 " --> pdb=" O VAL A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 218 removed outlier: 4.175A pdb=" N ALA A 214 " --> pdb=" O ASP A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 259 Processing helix chain 'A' and resid 265 through 295 removed outlier: 4.563A pdb=" N GLY A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N GLY A 275 " --> pdb=" O ILE A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 304 Processing helix chain 'A' and resid 312 through 336 removed outlier: 3.697A pdb=" N LEU A 316 " --> pdb=" O SER A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 361 removed outlier: 3.687A pdb=" N LEU A 349 " --> pdb=" O TYR A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 383 removed outlier: 3.514A pdb=" N THR A 383 " --> pdb=" O PHE A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 420 removed outlier: 3.516A pdb=" N SER A 402 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE A 406 " --> pdb=" O SER A 402 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 471 Proline residue: A 455 - end of helix Processing helix chain 'A' and resid 475 through 503 removed outlier: 3.693A pdb=" N ASN A 479 " --> pdb=" O PRO A 475 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA A 480 " --> pdb=" O HIS A 476 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR A 486 " --> pdb=" O LYS A 482 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE A 487 " --> pdb=" O TYR A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 531 removed outlier: 3.534A pdb=" N PHE A 510 " --> pdb=" O ASP A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 582 removed outlier: 3.989A pdb=" N TYR A 559 " --> pdb=" O GLN A 555 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N PHE A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ALA A 572 " --> pdb=" O ILE A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 618 Proline residue: A 598 - end of helix removed outlier: 3.579A pdb=" N PHE A 609 " --> pdb=" O PHE A 605 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASN A 614 " --> pdb=" O PHE A 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 36 removed outlier: 3.651A pdb=" N GLN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 99 Processing helix chain 'B' and resid 116 through 118 No H-bonds generated for 'chain 'B' and resid 116 through 118' Processing helix chain 'B' and resid 119 through 168 removed outlier: 3.787A pdb=" N LEU B 167 " --> pdb=" O HIS B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 181 Processing helix chain 'B' and resid 183 through 188 removed outlier: 3.929A pdb=" N CYS B 188 " --> pdb=" O PRO B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 206 removed outlier: 3.804A pdb=" N GLN B 193 " --> pdb=" O LYS B 189 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU B 205 " --> pdb=" O VAL B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 218 removed outlier: 4.174A pdb=" N ALA B 214 " --> pdb=" O ASP B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 259 Processing helix chain 'B' and resid 265 through 295 removed outlier: 4.563A pdb=" N GLY B 274 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N GLY B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 304 Processing helix chain 'B' and resid 312 through 336 removed outlier: 3.697A pdb=" N LEU B 316 " --> pdb=" O SER B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 361 removed outlier: 3.687A pdb=" N LEU B 349 " --> pdb=" O TYR B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 383 removed outlier: 3.515A pdb=" N THR B 383 " --> pdb=" O PHE B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 420 removed outlier: 3.517A pdb=" N SER B 402 " --> pdb=" O ASP B 398 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL B 405 " --> pdb=" O ASN B 401 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE B 406 " --> pdb=" O SER B 402 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 471 Proline residue: B 455 - end of helix Processing helix chain 'B' and resid 475 through 503 removed outlier: 3.693A pdb=" N ASN B 479 " --> pdb=" O PRO B 475 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA B 480 " --> pdb=" O HIS B 476 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR B 486 " --> pdb=" O LYS B 482 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE B 487 " --> pdb=" O TYR B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 531 removed outlier: 3.534A pdb=" N PHE B 510 " --> pdb=" O ASP B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 582 removed outlier: 3.989A pdb=" N TYR B 559 " --> pdb=" O GLN B 555 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N PHE B 571 " --> pdb=" O VAL B 567 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA B 572 " --> pdb=" O ILE B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 618 Proline residue: B 598 - end of helix removed outlier: 3.579A pdb=" N PHE B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASN B 614 " --> pdb=" O PHE B 610 " (cutoff:3.500A) 698 hydrogen bonds defined for protein. 2094 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: 1.55 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1997 1.33 - 1.45: 2525 1.45 - 1.57: 5370 1.57 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 9946 Sorted by residual: bond pdb=" N PRO A 338 " pdb=" CA PRO A 338 " ideal model delta sigma weight residual 1.465 1.422 0.043 1.19e-02 7.06e+03 1.32e+01 bond pdb=" N PRO B 338 " pdb=" CA PRO B 338 " ideal model delta sigma weight residual 1.465 1.423 0.043 1.19e-02 7.06e+03 1.29e+01 bond pdb=" CA ALA A 337 " pdb=" C ALA A 337 " ideal model delta sigma weight residual 1.522 1.492 0.030 9.10e-03 1.21e+04 1.09e+01 bond pdb=" CA ALA B 337 " pdb=" C ALA B 337 " ideal model delta sigma weight residual 1.522 1.493 0.029 9.10e-03 1.21e+04 1.02e+01 bond pdb=" N ILE B 339 " pdb=" CA ILE B 339 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.25e-02 6.40e+03 5.29e+00 ... (remaining 9941 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 12928 1.49 - 2.98: 420 2.98 - 4.47: 98 4.47 - 5.96: 20 5.96 - 7.45: 6 Bond angle restraints: 13472 Sorted by residual: angle pdb=" N PRO A 338 " pdb=" CA PRO A 338 " pdb=" C PRO A 338 " ideal model delta sigma weight residual 111.41 104.50 6.91 1.50e+00 4.44e-01 2.12e+01 angle pdb=" N PRO B 338 " pdb=" CA PRO B 338 " pdb=" C PRO B 338 " ideal model delta sigma weight residual 111.41 104.51 6.90 1.50e+00 4.44e-01 2.11e+01 angle pdb=" CA PRO A 338 " pdb=" C PRO A 338 " pdb=" O PRO A 338 " ideal model delta sigma weight residual 122.08 116.70 5.38 1.28e+00 6.10e-01 1.76e+01 angle pdb=" CA PRO B 338 " pdb=" C PRO B 338 " pdb=" O PRO B 338 " ideal model delta sigma weight residual 122.08 116.75 5.33 1.28e+00 6.10e-01 1.74e+01 angle pdb=" N PRO B 338 " pdb=" CA PRO B 338 " pdb=" CB PRO B 338 " ideal model delta sigma weight residual 103.38 99.83 3.55 1.05e+00 9.07e-01 1.14e+01 ... (remaining 13467 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.37: 4790 16.37 - 32.73: 712 32.73 - 49.10: 224 49.10 - 65.47: 38 65.47 - 81.83: 14 Dihedral angle restraints: 5778 sinusoidal: 2348 harmonic: 3430 Sorted by residual: dihedral pdb=" CA ALA A 473 " pdb=" C ALA A 473 " pdb=" N PHE A 474 " pdb=" CA PHE A 474 " ideal model delta harmonic sigma weight residual 180.00 155.73 24.27 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA ALA B 473 " pdb=" C ALA B 473 " pdb=" N PHE B 474 " pdb=" CA PHE B 474 " ideal model delta harmonic sigma weight residual 180.00 155.74 24.26 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA ILE B 20 " pdb=" C ILE B 20 " pdb=" N GLN B 21 " pdb=" CA GLN B 21 " ideal model delta harmonic sigma weight residual -180.00 -156.48 -23.52 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 5775 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1005 0.033 - 0.066: 323 0.066 - 0.099: 114 0.099 - 0.132: 14 0.132 - 0.165: 6 Chirality restraints: 1462 Sorted by residual: chirality pdb=" CB THR A 102 " pdb=" CA THR A 102 " pdb=" OG1 THR A 102 " pdb=" CG2 THR A 102 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 6.82e-01 chirality pdb=" CB THR B 102 " pdb=" CA THR B 102 " pdb=" OG1 THR B 102 " pdb=" CG2 THR B 102 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.16 2.00e-01 2.50e+01 6.75e-01 chirality pdb=" CA ILE A 342 " pdb=" N ILE A 342 " pdb=" C ILE A 342 " pdb=" CB ILE A 342 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.83e-01 ... (remaining 1459 not shown) Planarity restraints: 1674 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 335 " 0.019 2.00e-02 2.50e+03 4.00e-02 1.60e+01 pdb=" C PHE B 335 " -0.069 2.00e-02 2.50e+03 pdb=" O PHE B 335 " 0.026 2.00e-02 2.50e+03 pdb=" N PHE B 336 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 335 " -0.019 2.00e-02 2.50e+03 4.00e-02 1.60e+01 pdb=" C PHE A 335 " 0.069 2.00e-02 2.50e+03 pdb=" O PHE A 335 " -0.026 2.00e-02 2.50e+03 pdb=" N PHE A 336 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 338 " -0.015 2.00e-02 2.50e+03 3.11e-02 9.67e+00 pdb=" C PRO A 338 " 0.054 2.00e-02 2.50e+03 pdb=" O PRO A 338 " -0.020 2.00e-02 2.50e+03 pdb=" N ILE A 339 " -0.019 2.00e-02 2.50e+03 ... (remaining 1671 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 174 2.63 - 3.20: 9791 3.20 - 3.77: 16029 3.77 - 4.33: 19761 4.33 - 4.90: 32250 Nonbonded interactions: 78005 Sorted by model distance: nonbonded pdb=" OH TYR A 272 " pdb=" OG SER A 330 " model vdw 2.065 3.040 nonbonded pdb=" OH TYR B 272 " pdb=" OG SER B 330 " model vdw 2.065 3.040 nonbonded pdb=" O VAL A 182 " pdb=" OG1 THR A 187 " model vdw 2.131 3.040 nonbonded pdb=" O VAL B 182 " pdb=" OG1 THR B 187 " model vdw 2.131 3.040 nonbonded pdb=" O ASN B 310 " pdb=" ND2 ASN B 310 " model vdw 2.152 3.120 ... (remaining 78000 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' } 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 group one per residue 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: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.980 Find NCS groups from input model: 0.070 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: 0.010 Load rotamer database and sin/cos tables:1.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 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 : 0.004 0.043 9946 Z= 0.188 Angle : 0.679 7.451 13472 Z= 0.388 Chirality : 0.037 0.165 1462 Planarity : 0.004 0.040 1674 Dihedral : 17.428 81.832 3554 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 1.22 % Allowed : 9.35 % Favored : 89.42 % Rotamer: Outliers : 0.87 % Allowed : 26.12 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 are not related in a simple way. whole: 0.66 (0.25), residues: 1144 helix: 1.72 (0.17), residues: 844 sheet: None (None), residues: 0 loop : -3.54 (0.33), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 122 TYR 0.012 0.001 TYR A 518 PHE 0.020 0.001 PHE B 51 TRP 0.009 0.001 TRP A 175 HIS 0.003 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 9946) covalent geometry : angle 0.67891 (13472) hydrogen bonds : bond 0.08614 ( 698) hydrogen bonds : angle 5.38722 ( 2094) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 194 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 PHE cc_start: 0.8797 (p90) cc_final: 0.8550 (p90) REVERT: A 127 ASN cc_start: 0.8663 (m110) cc_final: 0.8459 (m110) REVERT: A 195 ILE cc_start: 0.9049 (tt) cc_final: 0.8671 (tt) REVERT: A 419 LEU cc_start: 0.8435 (mm) cc_final: 0.8118 (mp) REVERT: A 447 VAL cc_start: 0.8587 (m) cc_final: 0.8235 (p) REVERT: A 564 ILE cc_start: 0.8517 (tp) cc_final: 0.8157 (tp) REVERT: B 147 ASN cc_start: 0.9221 (m-40) cc_final: 0.8808 (m-40) REVERT: B 195 ILE cc_start: 0.9098 (tt) cc_final: 0.8775 (tt) REVERT: B 419 LEU cc_start: 0.8332 (mm) cc_final: 0.8079 (mp) REVERT: B 447 VAL cc_start: 0.8624 (m) cc_final: 0.8293 (p) REVERT: B 564 ILE cc_start: 0.8552 (tp) cc_final: 0.8201 (tp) outliers start: 9 outliers final: 2 residues processed: 198 average time/residue: 0.0959 time to fit residues: 25.7004 Evaluate side-chains 153 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 151 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain B residue 366 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.0470 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 0.0670 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.0060 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.0770 overall best weight: 0.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN ** A 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 GLN B 124 GLN ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.220422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.175727 restraints weight = 13853.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.174827 restraints weight = 18528.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.177741 restraints weight = 13892.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.177088 restraints weight = 9976.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.177556 restraints weight = 8440.753| |-----------------------------------------------------------------------------| r_work (final): 0.4446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9946 Z= 0.149 Angle : 0.727 10.354 13472 Z= 0.381 Chirality : 0.044 0.188 1462 Planarity : 0.004 0.037 1674 Dihedral : 5.028 39.532 1276 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.87 % Allowed : 9.53 % Favored : 89.60 % Rotamer: Outliers : 2.52 % Allowed : 26.70 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 are not related in a simple way. whole: 0.49 (0.25), residues: 1144 helix: 1.58 (0.17), residues: 850 sheet: None (None), residues: 0 loop : -3.67 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 308 TYR 0.022 0.002 TYR B 518 PHE 0.046 0.002 PHE A 156 TRP 0.013 0.001 TRP A 175 HIS 0.004 0.001 HIS B 163 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 9946) covalent geometry : angle 0.72747 (13472) hydrogen bonds : bond 0.04186 ( 698) hydrogen bonds : angle 5.03756 ( 2094) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 177 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 MET cc_start: 0.7707 (ppp) cc_final: 0.7482 (ppp) REVERT: A 58 PHE cc_start: 0.7412 (OUTLIER) cc_final: 0.7018 (t80) REVERT: A 419 LEU cc_start: 0.8407 (mm) cc_final: 0.7974 (mp) REVERT: A 447 VAL cc_start: 0.8601 (m) cc_final: 0.8281 (p) REVERT: A 564 ILE cc_start: 0.9001 (tp) cc_final: 0.8675 (tp) REVERT: B 51 PHE cc_start: 0.8186 (p90) cc_final: 0.7950 (p90) REVERT: B 58 PHE cc_start: 0.7487 (OUTLIER) cc_final: 0.6964 (t80) REVERT: B 419 LEU cc_start: 0.8354 (mm) cc_final: 0.7949 (mp) REVERT: B 447 VAL cc_start: 0.8589 (m) cc_final: 0.8324 (p) REVERT: B 564 ILE cc_start: 0.9031 (tp) cc_final: 0.8708 (tp) outliers start: 26 outliers final: 15 residues processed: 187 average time/residue: 0.0819 time to fit residues: 21.6554 Evaluate side-chains 171 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 563 ILE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 366 PHE Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain B residue 591 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 31 optimal weight: 0.2980 chunk 49 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 33 optimal weight: 0.0060 chunk 6 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 77 optimal weight: 0.0040 chunk 105 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 overall best weight: 0.4008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 ASN B 313 HIS ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4818 r_free = 0.4818 target = 0.225238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.181027 restraints weight = 13902.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.179559 restraints weight = 17311.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.182008 restraints weight = 13914.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.182086 restraints weight = 9016.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.182496 restraints weight = 8531.369| |-----------------------------------------------------------------------------| r_work (final): 0.4432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9946 Z= 0.145 Angle : 0.690 8.627 13472 Z= 0.364 Chirality : 0.042 0.159 1462 Planarity : 0.004 0.039 1674 Dihedral : 4.955 43.730 1276 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.87 % Allowed : 8.74 % Favored : 90.38 % Rotamer: Outliers : 4.17 % Allowed : 25.34 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 are not related in a simple way. whole: 0.48 (0.25), residues: 1144 helix: 1.53 (0.17), residues: 860 sheet: None (None), residues: 0 loop : -3.68 (0.33), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 308 TYR 0.017 0.001 TYR A 518 PHE 0.031 0.002 PHE A 156 TRP 0.025 0.001 TRP A 175 HIS 0.005 0.001 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 9946) covalent geometry : angle 0.68986 (13472) hydrogen bonds : bond 0.04055 ( 698) hydrogen bonds : angle 4.90367 ( 2094) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 170 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 TYR cc_start: 0.1356 (m-10) cc_final: 0.0953 (m-10) REVERT: A 58 PHE cc_start: 0.7479 (OUTLIER) cc_final: 0.7041 (t80) REVERT: A 419 LEU cc_start: 0.8206 (mm) cc_final: 0.7962 (mp) REVERT: A 447 VAL cc_start: 0.8605 (m) cc_final: 0.8329 (p) REVERT: A 517 PHE cc_start: 0.7210 (OUTLIER) cc_final: 0.6751 (t80) REVERT: A 564 ILE cc_start: 0.9004 (tp) cc_final: 0.8668 (tp) REVERT: B 19 TYR cc_start: 0.0837 (m-10) cc_final: 0.0457 (m-10) REVERT: B 58 PHE cc_start: 0.7577 (OUTLIER) cc_final: 0.7014 (t80) REVERT: B 419 LEU cc_start: 0.8179 (mm) cc_final: 0.7927 (mp) REVERT: B 447 VAL cc_start: 0.8616 (m) cc_final: 0.8320 (p) REVERT: B 517 PHE cc_start: 0.7278 (OUTLIER) cc_final: 0.6733 (t80) REVERT: B 564 ILE cc_start: 0.9061 (tp) cc_final: 0.8726 (tp) outliers start: 43 outliers final: 23 residues processed: 191 average time/residue: 0.0695 time to fit residues: 19.5421 Evaluate side-chains 187 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 366 PHE Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 517 PHE Chi-restraints excluded: chain B residue 581 SER Chi-restraints excluded: chain B residue 591 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 29 optimal weight: 0.5980 chunk 106 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 17 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 HIS ** A 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 ASN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4825 r_free = 0.4825 target = 0.231568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.178623 restraints weight = 13752.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.176049 restraints weight = 11973.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.179170 restraints weight = 10241.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.179241 restraints weight = 6942.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.179541 restraints weight = 6406.576| |-----------------------------------------------------------------------------| r_work (final): 0.4289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9946 Z= 0.160 Angle : 0.704 11.933 13472 Z= 0.367 Chirality : 0.044 0.159 1462 Planarity : 0.004 0.037 1674 Dihedral : 4.969 47.244 1276 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.87 % Allowed : 9.00 % Favored : 90.12 % Rotamer: Outliers : 5.05 % Allowed : 26.80 % Favored : 68.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 are not related in a simple way. whole: 0.52 (0.25), residues: 1144 helix: 1.51 (0.17), residues: 860 sheet: None (None), residues: 0 loop : -3.52 (0.33), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 308 TYR 0.028 0.001 TYR B 518 PHE 0.036 0.002 PHE B 135 TRP 0.028 0.001 TRP B 175 HIS 0.003 0.001 HIS B 179 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 9946) covalent geometry : angle 0.70435 (13472) hydrogen bonds : bond 0.04103 ( 698) hydrogen bonds : angle 4.80895 ( 2094) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 168 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.7737 (OUTLIER) cc_final: 0.7212 (t80) REVERT: A 59 PHE cc_start: 0.8168 (m-10) cc_final: 0.7889 (m-10) REVERT: A 332 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8102 (mm) REVERT: A 352 TYR cc_start: 0.7989 (m-80) cc_final: 0.7743 (m-10) REVERT: A 419 LEU cc_start: 0.8224 (mm) cc_final: 0.7988 (mp) REVERT: A 517 PHE cc_start: 0.7333 (OUTLIER) cc_final: 0.7017 (t80) REVERT: A 564 ILE cc_start: 0.9195 (tp) cc_final: 0.8872 (tp) REVERT: B 58 PHE cc_start: 0.7848 (OUTLIER) cc_final: 0.7108 (t80) REVERT: B 419 LEU cc_start: 0.8216 (mm) cc_final: 0.7980 (mp) REVERT: B 517 PHE cc_start: 0.7500 (OUTLIER) cc_final: 0.7111 (t80) REVERT: B 564 ILE cc_start: 0.9138 (tp) cc_final: 0.8831 (tp) outliers start: 52 outliers final: 31 residues processed: 195 average time/residue: 0.0704 time to fit residues: 20.0037 Evaluate side-chains 191 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 155 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 366 PHE Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 517 PHE Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 591 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 74 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 97 optimal weight: 0.0470 chunk 35 optimal weight: 0.0770 chunk 98 optimal weight: 7.9990 chunk 79 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 89 optimal weight: 7.9990 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 ASN ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4800 r_free = 0.4800 target = 0.224017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.178182 restraints weight = 14032.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.176610 restraints weight = 17266.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.179310 restraints weight = 13122.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.179605 restraints weight = 8318.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.179901 restraints weight = 8447.319| |-----------------------------------------------------------------------------| r_work (final): 0.4394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9946 Z= 0.144 Angle : 0.699 12.989 13472 Z= 0.366 Chirality : 0.042 0.151 1462 Planarity : 0.004 0.039 1674 Dihedral : 4.990 49.952 1276 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.70 % Allowed : 9.00 % Favored : 90.30 % Rotamer: Outliers : 4.37 % Allowed : 27.09 % Favored : 68.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 are not related in a simple way. whole: 0.60 (0.25), residues: 1144 helix: 1.60 (0.17), residues: 856 sheet: None (None), residues: 0 loop : -3.53 (0.32), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 308 TYR 0.022 0.001 TYR B 518 PHE 0.029 0.001 PHE B 156 TRP 0.022 0.001 TRP B 175 HIS 0.005 0.001 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 9946) covalent geometry : angle 0.69860 (13472) hydrogen bonds : bond 0.03971 ( 698) hydrogen bonds : angle 4.77771 ( 2094) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 168 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 MET cc_start: 0.7872 (ppp) cc_final: 0.7670 (ppp) REVERT: A 58 PHE cc_start: 0.7700 (OUTLIER) cc_final: 0.7148 (t80) REVERT: A 419 LEU cc_start: 0.8188 (mm) cc_final: 0.7949 (mp) REVERT: A 517 PHE cc_start: 0.7452 (OUTLIER) cc_final: 0.7068 (t80) REVERT: A 564 ILE cc_start: 0.9069 (tp) cc_final: 0.8744 (tp) REVERT: A 581 SER cc_start: 0.8095 (m) cc_final: 0.7758 (p) REVERT: B 58 PHE cc_start: 0.7687 (OUTLIER) cc_final: 0.6641 (t80) REVERT: B 160 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7368 (mm) REVERT: B 419 LEU cc_start: 0.8170 (mm) cc_final: 0.7941 (mp) REVERT: B 517 PHE cc_start: 0.7527 (OUTLIER) cc_final: 0.7107 (t80) REVERT: B 564 ILE cc_start: 0.9078 (tp) cc_final: 0.8757 (tp) REVERT: B 581 SER cc_start: 0.8055 (m) cc_final: 0.7760 (p) outliers start: 45 outliers final: 32 residues processed: 192 average time/residue: 0.0768 time to fit residues: 21.0156 Evaluate side-chains 198 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 161 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 366 PHE Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 517 PHE Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 619 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 0.0020 chunk 53 optimal weight: 1.9990 chunk 114 optimal weight: 0.4980 chunk 40 optimal weight: 0.6980 chunk 16 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 chunk 30 optimal weight: 0.5980 chunk 62 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 113 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN A 310 ASN ** A 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 GLN ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.223686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.178416 restraints weight = 13937.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.176376 restraints weight = 17957.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.179560 restraints weight = 12430.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.179375 restraints weight = 8332.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.180054 restraints weight = 7934.394| |-----------------------------------------------------------------------------| r_work (final): 0.4404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9946 Z= 0.142 Angle : 0.710 15.255 13472 Z= 0.369 Chirality : 0.042 0.153 1462 Planarity : 0.004 0.043 1674 Dihedral : 5.006 51.682 1276 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.87 % Allowed : 8.74 % Favored : 90.38 % Rotamer: Outliers : 5.05 % Allowed : 26.70 % Favored : 68.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 are not related in a simple way. whole: 0.63 (0.25), residues: 1144 helix: 1.62 (0.17), residues: 858 sheet: None (None), residues: 0 loop : -3.50 (0.32), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 308 TYR 0.021 0.001 TYR B 518 PHE 0.039 0.001 PHE B 51 TRP 0.017 0.001 TRP B 175 HIS 0.005 0.001 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 9946) covalent geometry : angle 0.71032 (13472) hydrogen bonds : bond 0.03920 ( 698) hydrogen bonds : angle 4.74532 ( 2094) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 171 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.7768 (OUTLIER) cc_final: 0.6950 (t80) REVERT: A 194 LEU cc_start: 0.7738 (mm) cc_final: 0.7179 (mm) REVERT: A 352 TYR cc_start: 0.7945 (m-80) cc_final: 0.7654 (m-80) REVERT: A 419 LEU cc_start: 0.8190 (mm) cc_final: 0.7919 (mp) REVERT: A 517 PHE cc_start: 0.7550 (OUTLIER) cc_final: 0.7169 (t80) REVERT: A 564 ILE cc_start: 0.9027 (tp) cc_final: 0.8690 (tp) REVERT: A 581 SER cc_start: 0.8042 (m) cc_final: 0.7702 (p) REVERT: B 160 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7490 (mm) REVERT: B 194 LEU cc_start: 0.7700 (mm) cc_final: 0.7142 (mm) REVERT: B 419 LEU cc_start: 0.8177 (mm) cc_final: 0.7957 (mp) REVERT: B 517 PHE cc_start: 0.7526 (OUTLIER) cc_final: 0.7145 (t80) REVERT: B 564 ILE cc_start: 0.9033 (tp) cc_final: 0.8708 (tp) REVERT: B 581 SER cc_start: 0.8049 (m) cc_final: 0.7732 (p) outliers start: 52 outliers final: 28 residues processed: 202 average time/residue: 0.0820 time to fit residues: 23.4495 Evaluate side-chains 193 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 186 TYR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 366 PHE Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 517 PHE Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 591 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 59 optimal weight: 10.0000 chunk 33 optimal weight: 0.5980 chunk 78 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 ASN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 ASN ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4816 r_free = 0.4816 target = 0.231296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.178960 restraints weight = 13789.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.176760 restraints weight = 11549.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.178576 restraints weight = 10094.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.179328 restraints weight = 7249.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.179584 restraints weight = 6698.078| |-----------------------------------------------------------------------------| r_work (final): 0.4281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9946 Z= 0.163 Angle : 0.749 15.458 13472 Z= 0.383 Chirality : 0.043 0.149 1462 Planarity : 0.004 0.041 1674 Dihedral : 5.058 53.511 1276 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.79 % Allowed : 8.39 % Favored : 90.82 % Rotamer: Outliers : 4.76 % Allowed : 25.73 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 are not related in a simple way. whole: 0.50 (0.25), residues: 1144 helix: 1.50 (0.17), residues: 858 sheet: None (None), residues: 0 loop : -3.48 (0.33), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 308 TYR 0.021 0.001 TYR B 518 PHE 0.041 0.002 PHE B 58 TRP 0.013 0.001 TRP B 175 HIS 0.004 0.001 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 9946) covalent geometry : angle 0.74945 (13472) hydrogen bonds : bond 0.04081 ( 698) hydrogen bonds : angle 4.78782 ( 2094) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 172 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 PHE cc_start: 0.8157 (t80) cc_final: 0.7946 (t80) REVERT: A 419 LEU cc_start: 0.8175 (mm) cc_final: 0.7901 (mp) REVERT: A 517 PHE cc_start: 0.7603 (OUTLIER) cc_final: 0.7329 (t80) REVERT: A 564 ILE cc_start: 0.9111 (tp) cc_final: 0.8808 (tp) REVERT: A 581 SER cc_start: 0.7984 (m) cc_final: 0.7633 (p) REVERT: B 156 PHE cc_start: 0.8159 (t80) cc_final: 0.7925 (t80) REVERT: B 160 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7429 (mm) REVERT: B 379 PHE cc_start: 0.8165 (t80) cc_final: 0.7919 (t80) REVERT: B 419 LEU cc_start: 0.8182 (mm) cc_final: 0.7955 (mp) REVERT: B 517 PHE cc_start: 0.7609 (OUTLIER) cc_final: 0.7299 (t80) REVERT: B 564 ILE cc_start: 0.9166 (tp) cc_final: 0.8864 (tp) REVERT: B 581 SER cc_start: 0.7906 (m) cc_final: 0.7630 (p) outliers start: 49 outliers final: 37 residues processed: 195 average time/residue: 0.0953 time to fit residues: 25.8626 Evaluate side-chains 201 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 161 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 619 ASN Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 366 PHE Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 517 PHE Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 591 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 73 optimal weight: 20.0000 chunk 22 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 9 optimal weight: 0.3980 chunk 110 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 ASN B 33 GLN B 193 GLN ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.232024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.179583 restraints weight = 13712.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.176293 restraints weight = 11770.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.179080 restraints weight = 10339.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.179529 restraints weight = 7096.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.180043 restraints weight = 6288.155| |-----------------------------------------------------------------------------| r_work (final): 0.4320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9946 Z= 0.157 Angle : 0.776 14.601 13472 Z= 0.402 Chirality : 0.045 0.352 1462 Planarity : 0.004 0.042 1674 Dihedral : 5.100 56.822 1276 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.70 % Allowed : 9.35 % Favored : 89.95 % Rotamer: Outliers : 4.66 % Allowed : 26.99 % Favored : 68.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 are not related in a simple way. whole: 0.59 (0.25), residues: 1144 helix: 1.56 (0.17), residues: 860 sheet: None (None), residues: 0 loop : -3.44 (0.33), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 308 TYR 0.020 0.001 TYR A 30 PHE 0.044 0.002 PHE B 51 TRP 0.011 0.001 TRP B 175 HIS 0.007 0.001 HIS B 125 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 9946) covalent geometry : angle 0.77587 (13472) hydrogen bonds : bond 0.04088 ( 698) hydrogen bonds : angle 4.80194 ( 2094) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 172 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 PHE cc_start: 0.8255 (m-80) cc_final: 0.7985 (m-80) REVERT: A 379 PHE cc_start: 0.8268 (t80) cc_final: 0.7962 (t80) REVERT: A 419 LEU cc_start: 0.8326 (mm) cc_final: 0.8066 (mp) REVERT: A 517 PHE cc_start: 0.7672 (OUTLIER) cc_final: 0.7451 (t80) REVERT: A 564 ILE cc_start: 0.9007 (tp) cc_final: 0.8688 (tp) REVERT: A 581 SER cc_start: 0.8002 (m) cc_final: 0.7625 (p) REVERT: B 160 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7684 (mm) REVERT: B 174 ASP cc_start: 0.7230 (OUTLIER) cc_final: 0.7028 (m-30) REVERT: B 379 PHE cc_start: 0.8281 (t80) cc_final: 0.7977 (t80) REVERT: B 419 LEU cc_start: 0.8387 (mm) cc_final: 0.8118 (mp) REVERT: B 517 PHE cc_start: 0.7698 (OUTLIER) cc_final: 0.7362 (t80) REVERT: B 564 ILE cc_start: 0.9056 (tp) cc_final: 0.8731 (tp) REVERT: B 581 SER cc_start: 0.8120 (m) cc_final: 0.7771 (p) REVERT: B 611 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7905 (ttt-90) outliers start: 48 outliers final: 37 residues processed: 199 average time/residue: 0.0895 time to fit residues: 25.0286 Evaluate side-chains 211 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 169 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain B residue 33 GLN Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 366 PHE Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 517 PHE Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 619 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 115 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 19 optimal weight: 0.0870 chunk 68 optimal weight: 3.9990 chunk 33 optimal weight: 0.0870 chunk 5 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 overall best weight: 1.0340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 ASN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 ASN ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4808 r_free = 0.4808 target = 0.230267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.179835 restraints weight = 13703.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.175886 restraints weight = 11521.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.179402 restraints weight = 10818.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.179335 restraints weight = 6811.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.179693 restraints weight = 6251.311| |-----------------------------------------------------------------------------| r_work (final): 0.4314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9946 Z= 0.180 Angle : 0.823 14.864 13472 Z= 0.417 Chirality : 0.046 0.437 1462 Planarity : 0.005 0.047 1674 Dihedral : 5.157 58.992 1276 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.70 % Allowed : 8.74 % Favored : 90.56 % Rotamer: Outliers : 3.88 % Allowed : 28.54 % Favored : 67.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 are not related in a simple way. whole: 0.59 (0.25), residues: 1144 helix: 1.55 (0.17), residues: 862 sheet: None (None), residues: 0 loop : -3.43 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 308 TYR 0.027 0.001 TYR A 30 PHE 0.074 0.002 PHE A 58 TRP 0.010 0.001 TRP B 175 HIS 0.004 0.001 HIS B 616 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 9946) covalent geometry : angle 0.82346 (13472) hydrogen bonds : bond 0.04263 ( 698) hydrogen bonds : angle 4.81018 ( 2094) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 169 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 PHE cc_start: 0.8105 (m-80) cc_final: 0.7838 (m-80) REVERT: A 379 PHE cc_start: 0.8235 (t80) cc_final: 0.7933 (t80) REVERT: A 419 LEU cc_start: 0.8286 (mm) cc_final: 0.8024 (mp) REVERT: A 517 PHE cc_start: 0.7696 (OUTLIER) cc_final: 0.7486 (t80) REVERT: A 564 ILE cc_start: 0.9057 (tp) cc_final: 0.8735 (tp) REVERT: A 581 SER cc_start: 0.7988 (m) cc_final: 0.7641 (p) REVERT: B 174 ASP cc_start: 0.7053 (OUTLIER) cc_final: 0.6838 (m-30) REVERT: B 379 PHE cc_start: 0.8310 (t80) cc_final: 0.7984 (t80) REVERT: B 419 LEU cc_start: 0.8301 (mm) cc_final: 0.8035 (mp) REVERT: B 517 PHE cc_start: 0.7769 (OUTLIER) cc_final: 0.7490 (t80) REVERT: B 564 ILE cc_start: 0.9084 (tp) cc_final: 0.8768 (tp) REVERT: B 581 SER cc_start: 0.8101 (m) cc_final: 0.7768 (p) outliers start: 40 outliers final: 33 residues processed: 191 average time/residue: 0.0816 time to fit residues: 22.0982 Evaluate side-chains 201 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 165 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 619 ASN Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 366 PHE Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 517 PHE Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 619 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 0.2980 chunk 96 optimal weight: 0.7980 chunk 115 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 111 optimal weight: 0.1980 chunk 2 optimal weight: 8.9990 chunk 9 optimal weight: 0.9990 chunk 4 optimal weight: 20.0000 chunk 71 optimal weight: 1.9990 chunk 15 optimal weight: 20.0000 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 ASN B 33 GLN ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.231874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.178976 restraints weight = 13745.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.176009 restraints weight = 11840.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.178310 restraints weight = 10800.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.178908 restraints weight = 7861.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.179316 restraints weight = 6805.518| |-----------------------------------------------------------------------------| r_work (final): 0.4276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9946 Z= 0.163 Angle : 0.852 18.539 13472 Z= 0.431 Chirality : 0.048 0.395 1462 Planarity : 0.005 0.055 1674 Dihedral : 5.165 57.252 1276 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.70 % Allowed : 9.18 % Favored : 90.12 % Rotamer: Outliers : 3.50 % Allowed : 28.93 % Favored : 67.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 are not related in a simple way. whole: 0.64 (0.25), residues: 1144 helix: 1.58 (0.17), residues: 862 sheet: None (None), residues: 0 loop : -3.43 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 308 TYR 0.040 0.002 TYR B 50 PHE 0.036 0.002 PHE A 59 TRP 0.011 0.001 TRP B 607 HIS 0.004 0.001 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 9946) covalent geometry : angle 0.85188 (13472) hydrogen bonds : bond 0.04259 ( 698) hydrogen bonds : angle 4.83140 ( 2094) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 173 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 PHE cc_start: 0.8031 (m-80) cc_final: 0.7757 (m-80) REVERT: A 137 GLU cc_start: 0.7985 (pp20) cc_final: 0.7619 (pp20) REVERT: A 138 PHE cc_start: 0.8086 (t80) cc_final: 0.7747 (t80) REVERT: A 308 ARG cc_start: 0.7829 (mmm160) cc_final: 0.7213 (mmm160) REVERT: A 379 PHE cc_start: 0.8115 (t80) cc_final: 0.7831 (t80) REVERT: A 419 LEU cc_start: 0.8241 (mm) cc_final: 0.7978 (mp) REVERT: A 564 ILE cc_start: 0.9093 (tp) cc_final: 0.8795 (tp) REVERT: A 581 SER cc_start: 0.8031 (m) cc_final: 0.7673 (p) REVERT: B 174 ASP cc_start: 0.7047 (OUTLIER) cc_final: 0.6828 (m-30) REVERT: B 379 PHE cc_start: 0.8170 (t80) cc_final: 0.7810 (t80) REVERT: B 419 LEU cc_start: 0.8274 (mm) cc_final: 0.8012 (mp) REVERT: B 517 PHE cc_start: 0.7832 (OUTLIER) cc_final: 0.7523 (t80) REVERT: B 564 ILE cc_start: 0.9137 (tp) cc_final: 0.8831 (tp) REVERT: B 581 SER cc_start: 0.8019 (m) cc_final: 0.7667 (p) outliers start: 36 outliers final: 29 residues processed: 193 average time/residue: 0.0867 time to fit residues: 23.3108 Evaluate side-chains 197 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 166 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 517 PHE Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 582 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 0 optimal weight: 9.9990 chunk 48 optimal weight: 0.0270 chunk 91 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 22 optimal weight: 0.0970 chunk 92 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 73 optimal weight: 0.0050 overall best weight: 0.2450 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4841 r_free = 0.4841 target = 0.234755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.183678 restraints weight = 13651.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.183454 restraints weight = 10617.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.184925 restraints weight = 9623.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.185217 restraints weight = 7279.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.185595 restraints weight = 6563.274| |-----------------------------------------------------------------------------| r_work (final): 0.4378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9946 Z= 0.152 Angle : 0.852 18.725 13472 Z= 0.431 Chirality : 0.047 0.410 1462 Planarity : 0.005 0.052 1674 Dihedral : 4.604 22.389 1272 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.70 % Allowed : 9.00 % Favored : 90.30 % Rotamer: Outliers : 3.50 % Allowed : 29.42 % Favored : 67.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 are not related in a simple way. whole: 0.62 (0.25), residues: 1144 helix: 1.60 (0.17), residues: 856 sheet: None (None), residues: 0 loop : -3.47 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 308 TYR 0.042 0.001 TYR A 30 PHE 0.035 0.001 PHE A 59 TRP 0.012 0.001 TRP A 607 HIS 0.004 0.001 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 9946) covalent geometry : angle 0.85165 (13472) hydrogen bonds : bond 0.04100 ( 698) hydrogen bonds : angle 4.80051 ( 2094) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1370.69 seconds wall clock time: 24 minutes 28.46 seconds (1468.46 seconds total)