Starting phenix.real_space_refine on Wed Sep 17 09:16:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dk9_46948/09_2025/9dk9_46948.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dk9_46948/09_2025/9dk9_46948.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dk9_46948/09_2025/9dk9_46948.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dk9_46948/09_2025/9dk9_46948.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dk9_46948/09_2025/9dk9_46948.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dk9_46948/09_2025/9dk9_46948.map" } resolution = 2.68 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 26 5.16 5 C 2474 2.51 5 N 657 2.21 5 O 659 1.98 5 H 3844 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7660 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 7660 Classifications: {'peptide': 517} Link IDs: {'PTRANS': 30, 'TRANS': 486} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 26 Time building chain proxies: 1.63, per 1000 atoms: 0.21 Number of scatterers: 7660 At special positions: 0 Unit cell: (111.055, 69.305, 70.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 26 16.00 O 659 8.00 N 657 7.00 C 2474 6.00 H 3844 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 116 " distance=2.03 Simple disulfide: pdb=" SG CYS A 88 " - pdb=" SG CYS A 139 " distance=2.03 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: 0.82 Conformation dependent library (CDL) restraints added in 347.5 milliseconds Enol-peptide restraints added in 1.2 microseconds 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 940 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 3 sheets defined 81.6% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 3 through 11 Processing helix chain 'A' and resid 14 through 37 removed outlier: 3.686A pdb=" N VAL A 26 " --> pdb=" O VAL A 22 " (cutoff:3.500A) Proline residue: A 27 - end of helix removed outlier: 3.840A pdb=" N TRP A 30 " --> pdb=" O VAL A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 42 Processing helix chain 'A' and resid 51 through 56 Processing helix chain 'A' and resid 56 through 63 removed outlier: 3.574A pdb=" N GLN A 60 " --> pdb=" O ASN A 56 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 75 removed outlier: 3.920A pdb=" N ALA A 74 " --> pdb=" O GLU A 70 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 100 removed outlier: 3.501A pdb=" N ASP A 100 " --> pdb=" O GLN A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 111 No H-bonds generated for 'chain 'A' and resid 109 through 111' Processing helix chain 'A' and resid 130 through 136 Processing helix chain 'A' and resid 138 through 142 Processing helix chain 'A' and resid 143 through 168 removed outlier: 3.520A pdb=" N TYR A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA A 161 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY A 164 " --> pdb=" O ALA A 160 " (cutoff:3.500A) Proline residue: A 165 - end of helix Processing helix chain 'A' and resid 172 through 191 removed outlier: 3.837A pdb=" N ALA A 191 " --> pdb=" O GLY A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 225 removed outlier: 3.599A pdb=" N GLY A 218 " --> pdb=" O MET A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 228 No H-bonds generated for 'chain 'A' and resid 226 through 228' Processing helix chain 'A' and resid 229 through 253 removed outlier: 3.534A pdb=" N VAL A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE A 241 " --> pdb=" O ASN A 237 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N HIS A 245 " --> pdb=" O PHE A 241 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR A 253 " --> pdb=" O ALA A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 267 Processing helix chain 'A' and resid 267 through 276 removed outlier: 4.382A pdb=" N LEU A 271 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 289 Processing helix chain 'A' and resid 292 through 307 Processing helix chain 'A' and resid 308 through 315 removed outlier: 3.923A pdb=" N GLY A 312 " --> pdb=" O LYS A 308 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A 315 " --> pdb=" O VAL A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 324 Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 336 through 340 removed outlier: 3.612A pdb=" N THR A 339 " --> pdb=" O SER A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 345 No H-bonds generated for 'chain 'A' and resid 343 through 345' Processing helix chain 'A' and resid 346 through 370 removed outlier: 4.010A pdb=" N PHE A 365 " --> pdb=" O GLY A 361 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASP A 370 " --> pdb=" O GLY A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 375 removed outlier: 4.100A pdb=" N LEU A 374 " --> pdb=" O ASP A 370 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY A 375 " --> pdb=" O LEU A 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 370 through 375' Processing helix chain 'A' and resid 377 through 403 removed outlier: 3.534A pdb=" N LEU A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ILE A 390 " --> pdb=" O GLY A 386 " (cutoff:3.500A) Proline residue: A 391 - end of helix removed outlier: 3.870A pdb=" N LEU A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU A 398 " --> pdb=" O ILE A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 426 removed outlier: 3.858A pdb=" N THR A 424 " --> pdb=" O ILE A 420 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 460 removed outlier: 3.681A pdb=" N ILE A 454 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLY A 457 " --> pdb=" O THR A 453 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU A 458 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 459 " --> pdb=" O TYR A 455 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N PHE A 460 " --> pdb=" O SER A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 486 Proline residue: A 484 - end of helix Processing helix chain 'A' and resid 487 through 492 removed outlier: 4.126A pdb=" N VAL A 491 " --> pdb=" O LEU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 512 removed outlier: 4.027A pdb=" N LEU A 498 " --> pdb=" O PRO A 494 " (cutoff:3.500A) Proline residue: A 505 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 80 removed outlier: 3.526A pdb=" N GLY A 84 " --> pdb=" O GLY A 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 91 251 hydrogen bonds defined for protein. 726 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: 1.81 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3835 1.03 - 1.23: 10 1.23 - 1.42: 1584 1.42 - 1.62: 2280 1.62 - 1.81: 39 Bond restraints: 7748 Sorted by residual: bond pdb=" CB GLN A 17 " pdb=" CG GLN A 17 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 9.01e-01 bond pdb=" CG GLN A 17 " pdb=" CD GLN A 17 " ideal model delta sigma weight residual 1.516 1.538 -0.022 2.50e-02 1.60e+03 7.74e-01 bond pdb=" N LYS A 145 " pdb=" CA LYS A 145 " ideal model delta sigma weight residual 1.463 1.457 0.006 6.90e-03 2.10e+04 7.19e-01 bond pdb=" CA VAL A 26 " pdb=" CB VAL A 26 " ideal model delta sigma weight residual 1.539 1.543 -0.004 5.40e-03 3.43e+04 6.58e-01 bond pdb=" CB GLN A 97 " pdb=" CG GLN A 97 " ideal model delta sigma weight residual 1.520 1.543 -0.023 3.00e-02 1.11e+03 6.05e-01 ... (remaining 7743 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.01: 12697 1.01 - 2.03: 1218 2.03 - 3.04: 81 3.04 - 4.06: 31 4.06 - 5.07: 5 Bond angle restraints: 14032 Sorted by residual: angle pdb=" C GLU A 223 " pdb=" N TRP A 224 " pdb=" CA TRP A 224 " ideal model delta sigma weight residual 120.58 117.01 3.57 1.71e+00 3.42e-01 4.37e+00 angle pdb=" CB GLN A 17 " pdb=" CG GLN A 17 " pdb=" CD GLN A 17 " ideal model delta sigma weight residual 112.60 116.11 -3.51 1.70e+00 3.46e-01 4.27e+00 angle pdb=" C LYS A 145 " pdb=" CA LYS A 145 " pdb=" CB LYS A 145 " ideal model delta sigma weight residual 113.57 110.41 3.16 1.57e+00 4.06e-01 4.06e+00 angle pdb=" CA GLN A 97 " pdb=" CB GLN A 97 " pdb=" CG GLN A 97 " ideal model delta sigma weight residual 114.10 118.11 -4.01 2.00e+00 2.50e-01 4.01e+00 angle pdb=" CA ARG A 284 " pdb=" CB ARG A 284 " pdb=" CG ARG A 284 " ideal model delta sigma weight residual 114.10 117.99 -3.89 2.00e+00 2.50e-01 3.79e+00 ... (remaining 14027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 3131 17.35 - 34.69: 322 34.69 - 52.04: 153 52.04 - 69.38: 42 69.38 - 86.73: 14 Dihedral angle restraints: 3662 sinusoidal: 1959 harmonic: 1703 Sorted by residual: dihedral pdb=" CB CYS A 49 " pdb=" SG CYS A 49 " pdb=" SG CYS A 116 " pdb=" CB CYS A 116 " ideal model delta sinusoidal sigma weight residual -86.00 -158.36 72.36 1 1.00e+01 1.00e-02 6.69e+01 dihedral pdb=" CG ARG A 256 " pdb=" CD ARG A 256 " pdb=" NE ARG A 256 " pdb=" CZ ARG A 256 " ideal model delta sinusoidal sigma weight residual -90.00 -39.75 -50.25 2 1.50e+01 4.44e-03 1.26e+01 dihedral pdb=" CA GLN A 87 " pdb=" CB GLN A 87 " pdb=" CG GLN A 87 " pdb=" CD GLN A 87 " ideal model delta sinusoidal sigma weight residual -180.00 -122.52 -57.48 3 1.50e+01 4.44e-03 9.44e+00 ... (remaining 3659 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 422 0.026 - 0.052: 122 0.052 - 0.078: 64 0.078 - 0.105: 26 0.105 - 0.131: 4 Chirality restraints: 638 Sorted by residual: chirality pdb=" CA VAL A 63 " pdb=" N VAL A 63 " pdb=" C VAL A 63 " pdb=" CB VAL A 63 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.27e-01 chirality pdb=" CA VAL A 121 " pdb=" N VAL A 121 " pdb=" C VAL A 121 " pdb=" CB VAL A 121 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.87e-01 chirality pdb=" CA VAL A 44 " pdb=" N VAL A 44 " pdb=" C VAL A 44 " pdb=" CB VAL A 44 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.34e-01 ... (remaining 635 not shown) Planarity restraints: 1161 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 17 " -0.009 2.00e-02 2.50e+03 1.83e-02 5.01e+00 pdb=" CD GLN A 17 " 0.039 2.00e-02 2.50e+03 pdb=" OE1 GLN A 17 " -0.018 2.00e-02 2.50e+03 pdb=" NE2 GLN A 17 " -0.006 2.00e-02 2.50e+03 pdb="HE21 GLN A 17 " -0.007 2.00e-02 2.50e+03 pdb="HE22 GLN A 17 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 256 " 0.124 9.50e-02 1.11e+02 4.16e-02 2.03e+00 pdb=" NE ARG A 256 " -0.009 2.00e-02 2.50e+03 pdb=" CZ ARG A 256 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 256 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 256 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG A 256 " -0.004 2.00e-02 2.50e+03 pdb="HH12 ARG A 256 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 256 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 256 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 26 " 0.023 5.00e-02 4.00e+02 3.46e-02 1.92e+00 pdb=" N PRO A 27 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 27 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 27 " 0.019 5.00e-02 4.00e+02 ... (remaining 1158 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.11: 133 2.11 - 2.73: 12835 2.73 - 3.35: 21951 3.35 - 3.98: 25744 3.98 - 4.60: 40723 Nonbonded interactions: 101386 Sorted by model distance: nonbonded pdb=" OE1 GLN A 97 " pdb=" H GLN A 97 " model vdw 1.487 2.450 nonbonded pdb=" OE1 GLU A 70 " pdb=" H GLU A 70 " model vdw 1.516 2.450 nonbonded pdb=" O GLN A 17 " pdb=" HG1 THR A 21 " model vdw 1.614 2.450 nonbonded pdb=" O TRP A 278 " pdb="HH22 ARG A 301 " model vdw 1.694 2.450 nonbonded pdb=" OD1 ASN A 377 " pdb=" H LEU A 380 " model vdw 1.712 2.450 ... (remaining 101381 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.630 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: 0.050 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 9.290 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6637 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3906 Z= 0.124 Angle : 0.557 5.071 5341 Z= 0.293 Chirality : 0.035 0.131 638 Planarity : 0.005 0.054 675 Dihedral : 17.614 86.730 1345 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.78 % Allowed : 34.64 % Favored : 64.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.38), residues: 515 helix: 1.53 (0.28), residues: 363 sheet: None (None), residues: 0 loop : -0.96 (0.47), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 256 TYR 0.009 0.001 TYR A 275 PHE 0.017 0.001 PHE A 243 TRP 0.008 0.001 TRP A 285 HIS 0.006 0.001 HIS A 86 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 3904) covalent geometry : angle 0.55711 ( 5337) SS BOND : bond 0.00200 ( 2) SS BOND : angle 0.46090 ( 4) hydrogen bonds : bond 0.17192 ( 251) hydrogen bonds : angle 5.29673 ( 726) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 31 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 98 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue LEU 321 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue SER 336 is missing expected H atoms. Skipping. Residue SER 435 is missing expected H atoms. Skipping. Residue LEU 464 is missing expected H atoms. Skipping. Evaluate side-chains 62 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.171 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: A 34 GLN cc_start: 0.7856 (tp40) cc_final: 0.7559 (mm110) REVERT: A 36 MET cc_start: 0.7777 (tpp) cc_final: 0.7548 (mmm) REVERT: A 147 MET cc_start: 0.6352 (ttp) cc_final: 0.5881 (tpt) REVERT: A 178 TRP cc_start: 0.6576 (t-100) cc_final: 0.5900 (t60) REVERT: A 242 SER cc_start: 0.6914 (OUTLIER) cc_final: 0.6541 (t) REVERT: A 257 ASP cc_start: 0.7065 (m-30) cc_final: 0.6659 (t70) outliers start: 3 outliers final: 1 residues processed: 62 average time/residue: 0.8339 time to fit residues: 54.1824 Evaluate side-chains 58 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 242 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 26 optimal weight: 0.4980 chunk 2 optimal weight: 0.4980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 0.0870 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 8.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.238635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.193201 restraints weight = 12405.166| |-----------------------------------------------------------------------------| r_work (start): 0.4323 rms_B_bonded: 2.59 r_work: 0.4224 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.4224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.0990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3906 Z= 0.132 Angle : 0.547 4.876 5341 Z= 0.286 Chirality : 0.036 0.134 638 Planarity : 0.005 0.039 675 Dihedral : 4.550 49.748 556 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 4.43 % Allowed : 30.99 % Favored : 64.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.38), residues: 515 helix: 1.59 (0.28), residues: 368 sheet: None (None), residues: 0 loop : -0.63 (0.52), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 256 TYR 0.013 0.001 TYR A 275 PHE 0.010 0.001 PHE A 362 TRP 0.005 0.001 TRP A 357 HIS 0.005 0.001 HIS A 86 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 3904) covalent geometry : angle 0.54749 ( 5337) SS BOND : bond 0.00074 ( 2) SS BOND : angle 0.49603 ( 4) hydrogen bonds : bond 0.05696 ( 251) hydrogen bonds : angle 4.23148 ( 726) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 31 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 98 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue LEU 321 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue SER 336 is missing expected H atoms. Skipping. Residue SER 435 is missing expected H atoms. Skipping. Residue LEU 464 is missing expected H atoms. Skipping. Evaluate side-chains 72 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 MET cc_start: 0.7160 (ttp) cc_final: 0.6713 (tpp) outliers start: 17 outliers final: 5 residues processed: 68 average time/residue: 0.6766 time to fit residues: 48.7385 Evaluate side-chains 59 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 378 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 23 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN A 149 GLN A 492 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.229163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.182245 restraints weight = 12492.556| |-----------------------------------------------------------------------------| r_work (start): 0.4227 rms_B_bonded: 2.56 r_work: 0.4124 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3906 Z= 0.165 Angle : 0.573 4.932 5341 Z= 0.298 Chirality : 0.038 0.131 638 Planarity : 0.005 0.040 675 Dihedral : 4.696 52.106 555 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 5.21 % Allowed : 28.12 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.38), residues: 515 helix: 1.29 (0.28), residues: 369 sheet: -3.49 (1.30), residues: 10 loop : -0.92 (0.52), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 230 TYR 0.013 0.002 TYR A 275 PHE 0.014 0.002 PHE A 362 TRP 0.008 0.001 TRP A 120 HIS 0.009 0.002 HIS A 86 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 3904) covalent geometry : angle 0.57284 ( 5337) SS BOND : bond 0.00191 ( 2) SS BOND : angle 0.54161 ( 4) hydrogen bonds : bond 0.05427 ( 251) hydrogen bonds : angle 4.12222 ( 726) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 31 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 98 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue LEU 321 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue SER 336 is missing expected H atoms. Skipping. Residue SER 435 is missing expected H atoms. Skipping. Residue LEU 464 is missing expected H atoms. Skipping. Evaluate side-chains 85 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 MET cc_start: 0.7264 (ttp) cc_final: 0.6725 (tpp) REVERT: A 224 TRP cc_start: 0.6905 (m100) cc_final: 0.6444 (m100) REVERT: A 430 MET cc_start: 0.5913 (mpp) cc_final: 0.5676 (mtt) outliers start: 20 outliers final: 7 residues processed: 80 average time/residue: 0.6382 time to fit residues: 54.0261 Evaluate side-chains 67 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 518 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 33 optimal weight: 0.0970 chunk 25 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 5 optimal weight: 0.0980 chunk 32 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.229535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.184539 restraints weight = 12441.844| |-----------------------------------------------------------------------------| r_work (start): 0.4243 rms_B_bonded: 2.46 r_work: 0.4138 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.4138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3906 Z= 0.114 Angle : 0.514 4.903 5341 Z= 0.261 Chirality : 0.035 0.129 638 Planarity : 0.004 0.039 675 Dihedral : 4.562 52.796 555 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 4.69 % Allowed : 27.34 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.38), residues: 515 helix: 1.51 (0.28), residues: 369 sheet: -3.47 (1.33), residues: 10 loop : -0.87 (0.52), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 256 TYR 0.013 0.001 TYR A 275 PHE 0.012 0.001 PHE A 362 TRP 0.007 0.001 TRP A 50 HIS 0.012 0.002 HIS A 86 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 3904) covalent geometry : angle 0.51433 ( 5337) SS BOND : bond 0.00098 ( 2) SS BOND : angle 0.41119 ( 4) hydrogen bonds : bond 0.04675 ( 251) hydrogen bonds : angle 3.93465 ( 726) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 31 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 98 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue LEU 321 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue SER 336 is missing expected H atoms. Skipping. Residue SER 435 is missing expected H atoms. Skipping. Residue LEU 464 is missing expected H atoms. Skipping. Evaluate side-chains 77 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.3007 (OUTLIER) cc_final: 0.2479 (tt) REVERT: A 147 MET cc_start: 0.7339 (ttp) cc_final: 0.6813 (tpp) REVERT: A 224 TRP cc_start: 0.6818 (m100) cc_final: 0.6123 (m100) REVERT: A 430 MET cc_start: 0.5912 (mpp) cc_final: 0.5603 (mtt) outliers start: 18 outliers final: 7 residues processed: 70 average time/residue: 0.6561 time to fit residues: 48.3549 Evaluate side-chains 62 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 518 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 47 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 20.0000 chunk 5 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 492 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.224040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.178376 restraints weight = 12481.360| |-----------------------------------------------------------------------------| r_work (start): 0.4199 rms_B_bonded: 2.47 r_work: 0.4095 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3906 Z= 0.158 Angle : 0.552 4.918 5341 Z= 0.287 Chirality : 0.037 0.140 638 Planarity : 0.005 0.041 675 Dihedral : 4.659 53.602 555 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.95 % Allowed : 27.08 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.37), residues: 515 helix: 1.34 (0.27), residues: 369 sheet: -3.86 (1.29), residues: 10 loop : -0.92 (0.51), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 347 TYR 0.014 0.002 TYR A 275 PHE 0.015 0.002 PHE A 362 TRP 0.008 0.001 TRP A 50 HIS 0.010 0.002 HIS A 86 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 3904) covalent geometry : angle 0.55263 ( 5337) SS BOND : bond 0.00157 ( 2) SS BOND : angle 0.27628 ( 4) hydrogen bonds : bond 0.05012 ( 251) hydrogen bonds : angle 4.00332 ( 726) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 31 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 98 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue LEU 321 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue SER 336 is missing expected H atoms. Skipping. Residue SER 435 is missing expected H atoms. Skipping. Residue LEU 464 is missing expected H atoms. Skipping. Evaluate side-chains 82 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.3160 (OUTLIER) cc_final: 0.2681 (tt) REVERT: A 147 MET cc_start: 0.7367 (ttp) cc_final: 0.6826 (tpp) REVERT: A 224 TRP cc_start: 0.6962 (m100) cc_final: 0.6546 (m100) REVERT: A 242 SER cc_start: 0.7480 (m) cc_final: 0.7121 (t) REVERT: A 279 LEU cc_start: 0.4835 (mt) cc_final: 0.3915 (pp) REVERT: A 430 MET cc_start: 0.6015 (mpp) cc_final: 0.5729 (mtt) outliers start: 19 outliers final: 7 residues processed: 75 average time/residue: 0.6299 time to fit residues: 49.9953 Evaluate side-chains 66 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 434 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 15 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.226577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.180864 restraints weight = 12449.801| |-----------------------------------------------------------------------------| r_work (start): 0.4198 rms_B_bonded: 2.46 r_work: 0.4092 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3906 Z= 0.123 Angle : 0.518 4.879 5341 Z= 0.265 Chirality : 0.036 0.128 638 Planarity : 0.004 0.039 675 Dihedral : 4.565 54.426 555 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.39 % Allowed : 27.86 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.38), residues: 515 helix: 1.49 (0.28), residues: 369 sheet: -3.89 (1.25), residues: 10 loop : -0.91 (0.51), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 230 TYR 0.013 0.001 TYR A 275 PHE 0.014 0.001 PHE A 362 TRP 0.007 0.001 TRP A 50 HIS 0.008 0.001 HIS A 86 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 3904) covalent geometry : angle 0.51762 ( 5337) SS BOND : bond 0.00158 ( 2) SS BOND : angle 0.34211 ( 4) hydrogen bonds : bond 0.04600 ( 251) hydrogen bonds : angle 3.93162 ( 726) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 31 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 98 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue LEU 321 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue SER 336 is missing expected H atoms. Skipping. Residue SER 435 is missing expected H atoms. Skipping. Residue LEU 464 is missing expected H atoms. Skipping. Evaluate side-chains 71 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.3225 (OUTLIER) cc_final: 0.2776 (tt) REVERT: A 147 MET cc_start: 0.7321 (ttp) cc_final: 0.6801 (tpp) REVERT: A 224 TRP cc_start: 0.6931 (m100) cc_final: 0.6160 (m100) REVERT: A 242 SER cc_start: 0.7393 (m) cc_final: 0.7117 (t) REVERT: A 279 LEU cc_start: 0.4862 (mt) cc_final: 0.3904 (pp) REVERT: A 430 MET cc_start: 0.5975 (mpp) cc_final: 0.5718 (mtt) outliers start: 13 outliers final: 9 residues processed: 66 average time/residue: 0.6595 time to fit residues: 46.0854 Evaluate side-chains 66 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 445 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 3 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 149 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.224915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.178937 restraints weight = 12395.044| |-----------------------------------------------------------------------------| r_work (start): 0.4193 rms_B_bonded: 2.47 r_work: 0.4089 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3906 Z= 0.130 Angle : 0.520 4.938 5341 Z= 0.267 Chirality : 0.036 0.130 638 Planarity : 0.004 0.038 675 Dihedral : 4.556 55.225 555 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.95 % Allowed : 26.82 % Favored : 68.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.38), residues: 515 helix: 1.45 (0.28), residues: 369 sheet: -3.91 (1.21), residues: 10 loop : -0.79 (0.51), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 347 TYR 0.013 0.002 TYR A 275 PHE 0.013 0.001 PHE A 362 TRP 0.007 0.001 TRP A 50 HIS 0.007 0.001 HIS A 86 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 3904) covalent geometry : angle 0.52062 ( 5337) SS BOND : bond 0.00190 ( 2) SS BOND : angle 0.30171 ( 4) hydrogen bonds : bond 0.04558 ( 251) hydrogen bonds : angle 3.92979 ( 726) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 31 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 98 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue LEU 321 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue SER 336 is missing expected H atoms. Skipping. Residue SER 435 is missing expected H atoms. Skipping. Residue LEU 464 is missing expected H atoms. Skipping. Evaluate side-chains 78 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 59 time to evaluate : 0.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 MET cc_start: 0.7310 (ttp) cc_final: 0.6806 (tpp) REVERT: A 224 TRP cc_start: 0.6919 (m100) cc_final: 0.6475 (m100) REVERT: A 242 SER cc_start: 0.7412 (m) cc_final: 0.7150 (t) REVERT: A 279 LEU cc_start: 0.4953 (mt) cc_final: 0.3988 (pp) REVERT: A 430 MET cc_start: 0.6015 (mpp) cc_final: 0.5740 (mtt) outliers start: 19 outliers final: 11 residues processed: 70 average time/residue: 0.6149 time to fit residues: 45.6213 Evaluate side-chains 69 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 434 ARG Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 453 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 8 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 32 optimal weight: 20.0000 chunk 28 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 33 optimal weight: 0.0170 overall best weight: 0.9220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 409 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.224953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.179026 restraints weight = 12594.240| |-----------------------------------------------------------------------------| r_work (start): 0.4196 rms_B_bonded: 2.48 r_work: 0.4092 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3906 Z= 0.125 Angle : 0.516 4.912 5341 Z= 0.263 Chirality : 0.036 0.133 638 Planarity : 0.004 0.040 675 Dihedral : 4.533 56.023 555 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.17 % Allowed : 27.86 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.38), residues: 515 helix: 1.46 (0.28), residues: 370 sheet: -3.78 (1.25), residues: 10 loop : -0.66 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 347 TYR 0.013 0.001 TYR A 275 PHE 0.013 0.001 PHE A 362 TRP 0.006 0.001 TRP A 50 HIS 0.007 0.001 HIS A 86 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 3904) covalent geometry : angle 0.51629 ( 5337) SS BOND : bond 0.00204 ( 2) SS BOND : angle 0.33713 ( 4) hydrogen bonds : bond 0.04407 ( 251) hydrogen bonds : angle 3.90959 ( 726) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 31 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 98 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue LEU 321 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue SER 336 is missing expected H atoms. Skipping. Residue SER 435 is missing expected H atoms. Skipping. Residue LEU 464 is missing expected H atoms. Skipping. Evaluate side-chains 80 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 MET cc_start: 0.7341 (ttp) cc_final: 0.6799 (tpp) REVERT: A 224 TRP cc_start: 0.6940 (m100) cc_final: 0.6496 (m100) REVERT: A 242 SER cc_start: 0.7449 (m) cc_final: 0.7183 (t) REVERT: A 279 LEU cc_start: 0.4912 (mt) cc_final: 0.3945 (pp) REVERT: A 430 MET cc_start: 0.5982 (mpp) cc_final: 0.5687 (mtt) outliers start: 16 outliers final: 9 residues processed: 75 average time/residue: 0.5998 time to fit residues: 47.8487 Evaluate side-chains 69 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 453 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 10 optimal weight: 20.0000 chunk 30 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.224391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.178342 restraints weight = 12375.589| |-----------------------------------------------------------------------------| r_work (start): 0.4184 rms_B_bonded: 2.47 r_work: 0.4079 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3958 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3906 Z= 0.131 Angle : 0.516 4.946 5341 Z= 0.266 Chirality : 0.036 0.128 638 Planarity : 0.004 0.043 675 Dihedral : 4.550 56.424 555 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 4.17 % Allowed : 27.86 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.38), residues: 515 helix: 1.45 (0.28), residues: 369 sheet: -3.81 (1.27), residues: 10 loop : -0.53 (0.53), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 90 TYR 0.013 0.002 TYR A 275 PHE 0.014 0.001 PHE A 362 TRP 0.007 0.001 TRP A 50 HIS 0.006 0.001 HIS A 86 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 3904) covalent geometry : angle 0.51609 ( 5337) SS BOND : bond 0.00227 ( 2) SS BOND : angle 0.30832 ( 4) hydrogen bonds : bond 0.04407 ( 251) hydrogen bonds : angle 3.91989 ( 726) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 31 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 98 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue LEU 321 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue SER 336 is missing expected H atoms. Skipping. Residue SER 435 is missing expected H atoms. Skipping. Residue LEU 464 is missing expected H atoms. Skipping. Evaluate side-chains 76 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.3374 (OUTLIER) cc_final: 0.2970 (tt) REVERT: A 147 MET cc_start: 0.7660 (ttp) cc_final: 0.6930 (tpp) REVERT: A 224 TRP cc_start: 0.7011 (m100) cc_final: 0.6207 (m100) REVERT: A 242 SER cc_start: 0.7526 (m) cc_final: 0.7290 (t) REVERT: A 279 LEU cc_start: 0.4940 (mt) cc_final: 0.3899 (pp) REVERT: A 430 MET cc_start: 0.6122 (mpp) cc_final: 0.5918 (mtt) outliers start: 16 outliers final: 9 residues processed: 72 average time/residue: 0.6086 time to fit residues: 46.6827 Evaluate side-chains 66 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 453 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 36 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 0.3980 chunk 42 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 6 optimal weight: 0.0670 overall best weight: 0.8522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.225732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.179311 restraints weight = 12296.049| |-----------------------------------------------------------------------------| r_work (start): 0.4188 rms_B_bonded: 2.47 r_work: 0.4083 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3962 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3906 Z= 0.121 Angle : 0.518 4.913 5341 Z= 0.263 Chirality : 0.036 0.129 638 Planarity : 0.004 0.040 675 Dihedral : 4.460 54.720 555 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.86 % Allowed : 29.69 % Favored : 67.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.38), residues: 515 helix: 1.52 (0.28), residues: 369 sheet: -3.71 (1.30), residues: 10 loop : -0.52 (0.54), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 90 TYR 0.013 0.001 TYR A 275 PHE 0.013 0.001 PHE A 362 TRP 0.006 0.001 TRP A 50 HIS 0.006 0.001 HIS A 86 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 3904) covalent geometry : angle 0.51838 ( 5337) SS BOND : bond 0.00215 ( 2) SS BOND : angle 0.36797 ( 4) hydrogen bonds : bond 0.04290 ( 251) hydrogen bonds : angle 3.89677 ( 726) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 31 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 98 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue LEU 321 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue SER 336 is missing expected H atoms. Skipping. Residue SER 435 is missing expected H atoms. Skipping. Residue LEU 464 is missing expected H atoms. Skipping. Evaluate side-chains 69 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 MET cc_start: 0.7653 (ttp) cc_final: 0.6913 (tpp) REVERT: A 224 TRP cc_start: 0.7018 (m100) cc_final: 0.6417 (m100) REVERT: A 242 SER cc_start: 0.7524 (m) cc_final: 0.7292 (t) REVERT: A 279 LEU cc_start: 0.4960 (mt) cc_final: 0.3923 (pp) REVERT: A 430 MET cc_start: 0.6146 (mpp) cc_final: 0.5945 (mtt) outliers start: 11 outliers final: 9 residues processed: 67 average time/residue: 0.5962 time to fit residues: 42.5648 Evaluate side-chains 66 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 453 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 25 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 26 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.226375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.180237 restraints weight = 12277.586| |-----------------------------------------------------------------------------| r_work (start): 0.4205 rms_B_bonded: 2.46 r_work: 0.4099 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3978 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.4333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3906 Z= 0.110 Angle : 0.506 4.961 5341 Z= 0.256 Chirality : 0.035 0.129 638 Planarity : 0.004 0.039 675 Dihedral : 3.529 17.167 552 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.60 % Allowed : 29.95 % Favored : 67.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.39), residues: 515 helix: 1.61 (0.28), residues: 369 sheet: -3.72 (1.29), residues: 10 loop : -0.62 (0.53), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 90 TYR 0.012 0.001 TYR A 275 PHE 0.013 0.001 PHE A 362 TRP 0.007 0.001 TRP A 278 HIS 0.005 0.001 HIS A 86 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 3904) covalent geometry : angle 0.50650 ( 5337) SS BOND : bond 0.00166 ( 2) SS BOND : angle 0.38351 ( 4) hydrogen bonds : bond 0.04085 ( 251) hydrogen bonds : angle 3.86383 ( 726) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2987.85 seconds wall clock time: 51 minutes 18.19 seconds (3078.19 seconds total)