Starting phenix.real_space_refine on Thu Jul 2 03:03:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9quj_53378/07_2026/9quj_53378.cif Found real_map, /net/cci-nas-00/data/ceres_data/9quj_53378/07_2026/9quj_53378.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9quj_53378/07_2026/9quj_53378.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9quj_53378/07_2026/9quj_53378.map" model { file = "/net/cci-nas-00/data/ceres_data/9quj_53378/07_2026/9quj_53378.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9quj_53378/07_2026/9quj_53378.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 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 P 40 5.49 5 S 16 5.16 5 C 3729 2.51 5 N 1027 2.21 5 O 1210 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6022 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 5203 Classifications: {'peptide': 627} Link IDs: {'PTRANS': 9, 'TRANS': 617} Chain: "B" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 410 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 409 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Time building chain proxies: 1.37, per 1000 atoms: 0.23 Number of scatterers: 6022 At special positions: 0 Unit cell: (73.14, 117.66, 111.3, 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 16 16.00 P 40 15.00 O 1210 8.00 N 1027 7.00 C 3729 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: 0.66 Conformation dependent library (CDL) restraints added in 191.1 milliseconds 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1226 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 7 sheets defined 54.9% alpha, 12.3% beta 17 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 7 through 10 Processing helix chain 'A' and resid 66 through 74 removed outlier: 3.553A pdb=" N ILE A 72 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR A 73 " --> pdb=" O ASN A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 121 through 130 Processing helix chain 'A' and resid 139 through 150 removed outlier: 3.708A pdb=" N ASP A 143 " --> pdb=" O ASN A 139 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN A 150 " --> pdb=" O PHE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 168 Processing helix chain 'A' and resid 177 through 187 removed outlier: 3.501A pdb=" N ASN A 187 " --> pdb=" O GLU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 233 removed outlier: 3.629A pdb=" N SER A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LEU A 219 " --> pdb=" O ASP A 215 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEU A 220 " --> pdb=" O SER A 216 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LYS A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU A 228 " --> pdb=" O LYS A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 256 removed outlier: 4.591A pdb=" N LEU A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) Proline residue: A 248 - end of helix Processing helix chain 'A' and resid 260 through 287 Processing helix chain 'A' and resid 295 through 307 Processing helix chain 'A' and resid 320 through 327 removed outlier: 3.611A pdb=" N LYS A 325 " --> pdb=" O ASP A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 350 Processing helix chain 'A' and resid 352 through 357 removed outlier: 3.917A pdb=" N HIS A 356 " --> pdb=" O LYS A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 Processing helix chain 'A' and resid 391 through 396 removed outlier: 3.614A pdb=" N ARG A 395 " --> pdb=" O GLN A 391 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU A 396 " --> pdb=" O LYS A 392 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 391 through 396' Processing helix chain 'A' and resid 413 through 424 Processing helix chain 'A' and resid 425 through 433 Processing helix chain 'A' and resid 437 through 448 Processing helix chain 'A' and resid 450 through 454 Processing helix chain 'A' and resid 455 through 470 removed outlier: 3.840A pdb=" N PHE A 467 " --> pdb=" O LYS A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 487 removed outlier: 3.589A pdb=" N LEU A 478 " --> pdb=" O ASN A 474 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS A 479 " --> pdb=" O TYR A 475 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASN A 480 " --> pdb=" O VAL A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 506 removed outlier: 4.013A pdb=" N HIS A 505 " --> pdb=" O SER A 501 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR A 506 " --> pdb=" O PHE A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 520 removed outlier: 3.637A pdb=" N TYR A 510 " --> pdb=" O TYR A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 566 Proline residue: A 546 - end of helix removed outlier: 3.594A pdb=" N ASP A 564 " --> pdb=" O VAL A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 609 removed outlier: 4.022A pdb=" N PHE A 608 " --> pdb=" O SER A 604 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 13 Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 29 removed outlier: 3.823A pdb=" N ASP A 24 " --> pdb=" O PHE A 40 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE A 40 " --> pdb=" O ASP A 24 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS A 38 " --> pdb=" O PHE A 26 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 57 through 60 removed outlier: 6.397A pdb=" N LYS A 135 " --> pdb=" O PHE A 158 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 363 through 364 removed outlier: 3.726A pdb=" N LYS A 258 " --> pdb=" O ILE A 399 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 367 through 369 removed outlier: 3.709A pdb=" N THR A 367 " --> pdb=" O GLU A 381 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 572 through 575 removed outlier: 6.923A pdb=" N ILE A 582 " --> pdb=" O ILE A 574 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 523 through 525 263 hydrogen bonds defined for protein. 750 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 43 hydrogen bonds 86 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 1.20 Time building geometry restraints manager: 0.84 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: 1614 1.33 - 1.45: 1136 1.45 - 1.57: 3355 1.57 - 1.69: 78 1.69 - 1.80: 23 Bond restraints: 6206 Sorted by residual: bond pdb=" C1' DT C 11 " pdb=" N1 DT C 11 " ideal model delta sigma weight residual 1.468 1.538 -0.070 1.40e-02 5.10e+03 2.48e+01 bond pdb=" C3' DT B 16 " pdb=" C2' DT B 16 " ideal model delta sigma weight residual 1.516 1.550 -0.034 8.00e-03 1.56e+04 1.80e+01 bond pdb=" C1' DC C 17 " pdb=" N1 DC C 17 " ideal model delta sigma weight residual 1.468 1.523 -0.055 1.40e-02 5.10e+03 1.55e+01 bond pdb=" C1' DT B 19 " pdb=" N1 DT B 19 " ideal model delta sigma weight residual 1.468 1.521 -0.053 1.40e-02 5.10e+03 1.43e+01 bond pdb=" C3' DT C 18 " pdb=" C2' DT C 18 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.39e+01 ... (remaining 6201 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 7949 1.16 - 2.32: 454 2.32 - 3.48: 102 3.48 - 4.64: 19 4.64 - 5.79: 6 Bond angle restraints: 8530 Sorted by residual: angle pdb=" N3 DT B 16 " pdb=" C4 DT B 16 " pdb=" O4 DT B 16 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.01e+01 angle pdb=" N3 DT C 11 " pdb=" C4 DT C 11 " pdb=" O4 DT C 11 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 angle pdb=" N3 DT C 26 " pdb=" C4 DT C 26 " pdb=" O4 DT C 26 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.86e+01 angle pdb=" C4' DT C 18 " pdb=" O4' DT C 18 " pdb=" C1' DT C 18 " ideal model delta sigma weight residual 110.10 105.85 4.25 1.00e+00 1.00e+00 1.80e+01 angle pdb=" O4 DT B 16 " pdb=" C4 DT B 16 " pdb=" C5 DT B 16 " ideal model delta sigma weight residual 124.90 121.96 2.94 7.00e-01 2.04e+00 1.76e+01 ... (remaining 8525 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.01: 3423 28.01 - 56.02: 239 56.02 - 84.03: 25 84.03 - 112.04: 0 112.04 - 140.05: 1 Dihedral angle restraints: 3688 sinusoidal: 1805 harmonic: 1883 Sorted by residual: dihedral pdb=" CA LYS A 382 " pdb=" C LYS A 382 " pdb=" N PRO A 383 " pdb=" CA PRO A 383 " ideal model delta harmonic sigma weight residual 180.00 156.35 23.65 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" C4' DA B 13 " pdb=" C3' DA B 13 " pdb=" O3' DA B 13 " pdb=" P DG B 14 " ideal model delta sinusoidal sigma weight residual 220.00 79.95 140.05 1 3.50e+01 8.16e-04 1.38e+01 dihedral pdb=" CA ALA A 464 " pdb=" C ALA A 464 " pdb=" N ILE A 465 " pdb=" CA ILE A 465 " ideal model delta harmonic sigma weight residual -180.00 -163.42 -16.58 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 3685 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 599 0.036 - 0.073: 239 0.073 - 0.109: 67 0.109 - 0.145: 42 0.145 - 0.182: 10 Chirality restraints: 957 Sorted by residual: chirality pdb=" C3' DT B 22 " pdb=" C4' DT B 22 " pdb=" O3' DT B 22 " pdb=" C2' DT B 22 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.24e-01 chirality pdb=" C3' DC C 15 " pdb=" C4' DC C 15 " pdb=" O3' DC C 15 " pdb=" C2' DC C 15 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.18 2.00e-01 2.50e+01 7.69e-01 chirality pdb=" C3' DG B 23 " pdb=" C4' DG B 23 " pdb=" O3' DG B 23 " pdb=" C2' DG B 23 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.16e-01 ... (remaining 954 not shown) Planarity restraints: 950 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 247 " -0.031 5.00e-02 4.00e+02 4.65e-02 3.47e+00 pdb=" N PRO A 248 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 248 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 248 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 382 " 0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO A 383 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 383 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 383 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA B 17 " 0.019 2.00e-02 2.50e+03 8.75e-03 2.10e+00 pdb=" N9 DA B 17 " -0.020 2.00e-02 2.50e+03 pdb=" C8 DA B 17 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DA B 17 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA B 17 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA B 17 " 0.007 2.00e-02 2.50e+03 pdb=" N6 DA B 17 " 0.003 2.00e-02 2.50e+03 pdb=" N1 DA B 17 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA B 17 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DA B 17 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DA B 17 " -0.001 2.00e-02 2.50e+03 ... (remaining 947 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 264 2.71 - 3.26: 6108 3.26 - 3.81: 9992 3.81 - 4.35: 11877 4.35 - 4.90: 19499 Nonbonded interactions: 47740 Sorted by model distance: nonbonded pdb=" OD1 ASP A 251 " pdb=" ND2 ASN A 255 " model vdw 2.168 3.120 nonbonded pdb=" OG1 THR A 86 " pdb=" OE1 GLU A 93 " model vdw 2.247 3.040 nonbonded pdb=" O LEU A 438 " pdb=" OG1 THR A 442 " model vdw 2.251 3.040 nonbonded pdb=" NZ LYS A 283 " pdb=" O ILE A 291 " model vdw 2.271 3.120 nonbonded pdb=" OE1 GLN A 84 " pdb=" CH2 TRP A 199 " model vdw 2.288 3.340 ... (remaining 47735 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 6 through 10 or resid 12 through 13 or resid 15 through 25 \ )) selection = (chain 'C' and (resid 10 through 20 or resid 22 through 23 or resid 25 through 2 \ 8 or (resid 29 and (name P or name OP1 or name OP2 or name O5' or name C5' or na \ me C4' or name O4' or name C3' or name C2' or name C1' or name N1 or name C2 or \ name O2 or name N3 or name C4 or name N4 or name C5 or name C6 )))) } 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.140 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 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 : 0.006 0.070 6206 Z= 0.392 Angle : 0.648 5.795 8530 Z= 0.485 Chirality : 0.049 0.182 957 Planarity : 0.003 0.047 950 Dihedral : 17.080 140.049 2462 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.04 % Favored : 96.80 % Rotamer: Outliers : 0.51 % Allowed : 6.44 % Favored : 93.05 % 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 are not related in a simple way. whole: 0.36 (0.35), residues: 625 helix: 0.88 (0.30), residues: 302 sheet: -0.49 (0.63), residues: 68 loop : -0.19 (0.42), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 390 TYR 0.014 0.001 TYR A 110 PHE 0.014 0.002 PHE A 142 TRP 0.007 0.002 TRP A 199 HIS 0.004 0.001 HIS A 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.39 ( 6206) covalent geometry : angle 0.64823 / 0.48 ( 8530) hydrogen bonds : bond 0.15833 / 9.28 ( 306) hydrogen bonds : angle 6.69703 / 4.66 ( 836) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 199 time to evaluate : 0.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.8437 (tt) cc_final: 0.7963 (pt) REVERT: A 21 LYS cc_start: 0.8087 (tttp) cc_final: 0.7087 (tttt) REVERT: A 78 TYR cc_start: 0.8014 (p90) cc_final: 0.7477 (p90) REVERT: A 93 GLU cc_start: 0.6852 (mm-30) cc_final: 0.6509 (mm-30) REVERT: A 170 ASN cc_start: 0.6832 (t0) cc_final: 0.6504 (t0) REVERT: A 200 ASN cc_start: 0.7922 (t0) cc_final: 0.7708 (t0) REVERT: A 210 PHE cc_start: 0.6774 (m-80) cc_final: 0.6529 (m-80) REVERT: A 321 ASP cc_start: 0.7134 (t70) cc_final: 0.6930 (t0) REVERT: A 332 GLU cc_start: 0.6659 (tp30) cc_final: 0.6459 (tp30) REVERT: A 335 SER cc_start: 0.8082 (t) cc_final: 0.7879 (p) REVERT: A 369 ASN cc_start: 0.7769 (m-40) cc_final: 0.7409 (m-40) REVERT: A 372 LYS cc_start: 0.7716 (mttm) cc_final: 0.7387 (mttm) REVERT: A 421 GLU cc_start: 0.7871 (tp30) cc_final: 0.7453 (tp30) REVERT: A 481 TYR cc_start: 0.8353 (t80) cc_final: 0.8080 (t80) REVERT: A 510 TYR cc_start: 0.7509 (t80) cc_final: 0.7107 (t80) REVERT: A 514 ASN cc_start: 0.7794 (m-40) cc_final: 0.7471 (m-40) REVERT: A 523 GLN cc_start: 0.7675 (tm-30) cc_final: 0.7315 (tm-30) outliers start: 3 outliers final: 0 residues processed: 201 average time/residue: 0.0961 time to fit residues: 23.9012 Evaluate side-chains 186 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.0020 chunk 27 optimal weight: 0.6980 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 ASN ** A 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 ASN A 151 ASN A 172 ASN A 236 HIS A 255 ASN A 386 GLN A 387 GLN A 513 HIS A 623 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.156523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.126619 restraints weight = 9006.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.130078 restraints weight = 4420.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.132273 restraints weight = 2610.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.133633 restraints weight = 1778.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.134584 restraints weight = 1372.142| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6206 Z= 0.198 Angle : 0.612 6.144 8530 Z= 0.359 Chirality : 0.046 0.166 957 Planarity : 0.004 0.053 950 Dihedral : 20.223 138.063 1100 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.88 % Favored : 96.96 % Rotamer: Outliers : 2.71 % Allowed : 14.07 % Favored : 83.22 % 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 are not related in a simple way. whole: 0.37 (0.35), residues: 625 helix: 0.87 (0.30), residues: 308 sheet: -0.62 (0.60), residues: 76 loop : -0.11 (0.44), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 214 TYR 0.008 0.001 TYR A 499 PHE 0.015 0.002 PHE A 411 TRP 0.021 0.004 TRP A 624 HIS 0.004 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.20 ( 6206) covalent geometry : angle 0.61225 / 0.36 ( 8530) hydrogen bonds : bond 0.05817 / 3.55 ( 306) hydrogen bonds : angle 5.31959 / 3.69 ( 836) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 179 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.8198 (tt) cc_final: 0.7785 (pt) REVERT: A 48 LYS cc_start: 0.8357 (tttt) cc_final: 0.8119 (tptt) REVERT: A 68 ASN cc_start: 0.7984 (m-40) cc_final: 0.7771 (m-40) REVERT: A 78 TYR cc_start: 0.8001 (p90) cc_final: 0.7588 (p90) REVERT: A 103 GLU cc_start: 0.7765 (tt0) cc_final: 0.7451 (tt0) REVERT: A 168 ASP cc_start: 0.6544 (OUTLIER) cc_final: 0.6290 (m-30) REVERT: A 170 ASN cc_start: 0.6786 (t0) cc_final: 0.6450 (t0) REVERT: A 200 ASN cc_start: 0.7874 (t0) cc_final: 0.7638 (t0) REVERT: A 210 PHE cc_start: 0.6866 (m-80) cc_final: 0.6573 (m-80) REVERT: A 251 ASP cc_start: 0.7746 (t70) cc_final: 0.7151 (t70) REVERT: A 253 GLU cc_start: 0.7485 (mt-10) cc_final: 0.6964 (mt-10) REVERT: A 287 LYS cc_start: 0.8400 (mmmt) cc_final: 0.7938 (mmmt) REVERT: A 335 SER cc_start: 0.8146 (t) cc_final: 0.7888 (p) REVERT: A 369 ASN cc_start: 0.7721 (m-40) cc_final: 0.7292 (m-40) REVERT: A 372 LYS cc_start: 0.7715 (mttm) cc_final: 0.7355 (mttm) REVERT: A 378 PHE cc_start: 0.7694 (m-80) cc_final: 0.7348 (m-80) REVERT: A 481 TYR cc_start: 0.8305 (t80) cc_final: 0.8030 (t80) REVERT: A 510 TYR cc_start: 0.7436 (t80) cc_final: 0.6952 (t80) REVERT: A 514 ASN cc_start: 0.7742 (m-40) cc_final: 0.7435 (m-40) REVERT: A 523 GLN cc_start: 0.7717 (tm-30) cc_final: 0.7335 (tm-30) REVERT: A 619 LYS cc_start: 0.7371 (pttm) cc_final: 0.7155 (pttp) outliers start: 16 outliers final: 10 residues processed: 185 average time/residue: 0.0984 time to fit residues: 22.5931 Evaluate side-chains 181 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 170 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 588 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 30 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 63 optimal weight: 10.0000 chunk 58 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 ASN A 306 ASN ** A 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.156311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.126176 restraints weight = 9083.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.129729 restraints weight = 4444.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.132021 restraints weight = 2614.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.133417 restraints weight = 1769.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.134379 restraints weight = 1357.831| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6206 Z= 0.207 Angle : 0.588 5.972 8530 Z= 0.344 Chirality : 0.046 0.174 957 Planarity : 0.004 0.057 950 Dihedral : 20.478 136.478 1100 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.20 % Favored : 96.64 % Rotamer: Outliers : 4.41 % Allowed : 14.58 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.34), residues: 625 helix: 0.84 (0.29), residues: 309 sheet: -0.72 (0.59), residues: 76 loop : -0.19 (0.44), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 459 TYR 0.012 0.001 TYR A 471 PHE 0.013 0.002 PHE A 58 TRP 0.009 0.002 TRP A 624 HIS 0.004 0.001 HIS A 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.21 ( 6206) covalent geometry : angle 0.58805 / 0.34 ( 8530) hydrogen bonds : bond 0.05399 / 3.27 ( 306) hydrogen bonds : angle 5.07464 / 3.52 ( 836) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 185 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.7464 (tttm) cc_final: 0.6958 (tttp) REVERT: A 13 ILE cc_start: 0.8198 (tt) cc_final: 0.7812 (pt) REVERT: A 21 LYS cc_start: 0.8135 (tttp) cc_final: 0.7828 (tttp) REVERT: A 48 LYS cc_start: 0.8378 (tttt) cc_final: 0.8099 (tptt) REVERT: A 68 ASN cc_start: 0.7996 (m-40) cc_final: 0.7756 (m-40) REVERT: A 78 TYR cc_start: 0.7975 (p90) cc_final: 0.7558 (p90) REVERT: A 84 GLN cc_start: 0.7524 (mm-40) cc_final: 0.7271 (mm-40) REVERT: A 103 GLU cc_start: 0.7734 (tt0) cc_final: 0.7427 (tt0) REVERT: A 168 ASP cc_start: 0.6457 (OUTLIER) cc_final: 0.6243 (m-30) REVERT: A 170 ASN cc_start: 0.6769 (t0) cc_final: 0.6442 (t0) REVERT: A 200 ASN cc_start: 0.7889 (t0) cc_final: 0.7624 (t0) REVERT: A 210 PHE cc_start: 0.6893 (m-80) cc_final: 0.6599 (m-80) REVERT: A 335 SER cc_start: 0.8101 (t) cc_final: 0.7897 (p) REVERT: A 353 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7840 (mp) REVERT: A 366 THR cc_start: 0.8662 (OUTLIER) cc_final: 0.8304 (t) REVERT: A 369 ASN cc_start: 0.7726 (m-40) cc_final: 0.7188 (m-40) REVERT: A 372 LYS cc_start: 0.7760 (mttm) cc_final: 0.7379 (mttm) REVERT: A 378 PHE cc_start: 0.7712 (m-80) cc_final: 0.7386 (m-80) REVERT: A 481 TYR cc_start: 0.8289 (t80) cc_final: 0.8008 (t80) REVERT: A 523 GLN cc_start: 0.7695 (tm-30) cc_final: 0.7331 (tm-30) outliers start: 26 outliers final: 13 residues processed: 195 average time/residue: 0.0904 time to fit residues: 21.9161 Evaluate side-chains 197 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 181 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 588 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 62 optimal weight: 30.0000 chunk 43 optimal weight: 0.4980 chunk 34 optimal weight: 0.9980 chunk 42 optimal weight: 0.0030 chunk 61 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 47 optimal weight: 0.4980 chunk 35 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 ASN A 513 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.158821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.128902 restraints weight = 9002.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.132411 restraints weight = 4393.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.134636 restraints weight = 2581.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.136105 restraints weight = 1754.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.137046 restraints weight = 1332.443| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6206 Z= 0.150 Angle : 0.555 6.268 8530 Z= 0.325 Chirality : 0.044 0.202 957 Planarity : 0.003 0.060 950 Dihedral : 20.592 135.941 1100 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.92 % Favored : 97.92 % Rotamer: Outliers : 4.07 % Allowed : 16.44 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.35), residues: 625 helix: 1.06 (0.30), residues: 308 sheet: -0.78 (0.58), residues: 76 loop : -0.09 (0.43), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 459 TYR 0.008 0.001 TYR A 346 PHE 0.012 0.002 PHE A 58 TRP 0.006 0.001 TRP A 624 HIS 0.003 0.001 HIS A 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.15 ( 6206) covalent geometry : angle 0.55451 / 0.32 ( 8530) hydrogen bonds : bond 0.04776 / 2.90 ( 306) hydrogen bonds : angle 4.89951 / 3.40 ( 836) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 179 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.8093 (tttp) cc_final: 0.7840 (tttp) REVERT: A 48 LYS cc_start: 0.8392 (tttt) cc_final: 0.8112 (tptt) REVERT: A 68 ASN cc_start: 0.7959 (m-40) cc_final: 0.7706 (m-40) REVERT: A 78 TYR cc_start: 0.7949 (p90) cc_final: 0.7357 (p90) REVERT: A 117 LYS cc_start: 0.7301 (mmtm) cc_final: 0.6821 (mmtm) REVERT: A 118 LYS cc_start: 0.7602 (mmmt) cc_final: 0.7111 (mmmt) REVERT: A 170 ASN cc_start: 0.6761 (t0) cc_final: 0.6234 (t0) REVERT: A 200 ASN cc_start: 0.7843 (t0) cc_final: 0.7618 (t0) REVERT: A 210 PHE cc_start: 0.6856 (m-80) cc_final: 0.6531 (m-80) REVERT: A 251 ASP cc_start: 0.7743 (t0) cc_final: 0.7296 (t70) REVERT: A 284 LYS cc_start: 0.7820 (mmmm) cc_final: 0.7442 (mmmm) REVERT: A 321 ASP cc_start: 0.7239 (t0) cc_final: 0.6837 (t70) REVERT: A 335 SER cc_start: 0.8085 (t) cc_final: 0.7860 (p) REVERT: A 353 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7810 (mp) REVERT: A 366 THR cc_start: 0.8578 (OUTLIER) cc_final: 0.8214 (t) REVERT: A 369 ASN cc_start: 0.7553 (m-40) cc_final: 0.7155 (m-40) REVERT: A 372 LYS cc_start: 0.7739 (mttm) cc_final: 0.7383 (mttm) REVERT: A 378 PHE cc_start: 0.7747 (m-80) cc_final: 0.7379 (m-80) REVERT: A 481 TYR cc_start: 0.8297 (t80) cc_final: 0.8005 (t80) REVERT: A 523 GLN cc_start: 0.7671 (tm-30) cc_final: 0.7321 (tm-30) outliers start: 24 outliers final: 13 residues processed: 186 average time/residue: 0.0913 time to fit residues: 21.0456 Evaluate side-chains 188 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 173 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 519 LYS Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 588 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 44 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 45 optimal weight: 0.0570 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 ASN A 296 GLN A 513 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.158093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.128282 restraints weight = 9088.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.131812 restraints weight = 4428.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.134086 restraints weight = 2598.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.135532 restraints weight = 1759.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.136478 restraints weight = 1336.160| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6206 Z= 0.175 Angle : 0.563 6.596 8530 Z= 0.326 Chirality : 0.044 0.160 957 Planarity : 0.003 0.060 950 Dihedral : 20.677 135.744 1100 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.40 % Favored : 97.44 % Rotamer: Outliers : 4.07 % Allowed : 17.29 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.35), residues: 625 helix: 1.09 (0.30), residues: 310 sheet: -0.77 (0.58), residues: 76 loop : -0.03 (0.44), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 337 TYR 0.009 0.001 TYR A 73 PHE 0.013 0.002 PHE A 58 TRP 0.006 0.002 TRP A 624 HIS 0.004 0.001 HIS A 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.18 ( 6206) covalent geometry : angle 0.56312 / 0.33 ( 8530) hydrogen bonds : bond 0.04763 / 2.89 ( 306) hydrogen bonds : angle 4.80082 / 3.32 ( 836) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 177 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.8195 (tttp) cc_final: 0.7915 (tttp) REVERT: A 48 LYS cc_start: 0.8398 (tttt) cc_final: 0.8122 (tptt) REVERT: A 68 ASN cc_start: 0.7970 (m-40) cc_final: 0.7760 (m-40) REVERT: A 78 TYR cc_start: 0.7958 (p90) cc_final: 0.7342 (p90) REVERT: A 84 GLN cc_start: 0.7539 (mm-40) cc_final: 0.7289 (mm-40) REVERT: A 117 LYS cc_start: 0.7291 (mmtm) cc_final: 0.6981 (mmtm) REVERT: A 170 ASN cc_start: 0.6739 (t0) cc_final: 0.6213 (t0) REVERT: A 200 ASN cc_start: 0.7859 (t0) cc_final: 0.7638 (t0) REVERT: A 210 PHE cc_start: 0.6884 (m-80) cc_final: 0.6564 (m-80) REVERT: A 251 ASP cc_start: 0.7692 (t0) cc_final: 0.7276 (t70) REVERT: A 284 LYS cc_start: 0.7827 (mmmm) cc_final: 0.7449 (mmmm) REVERT: A 321 ASP cc_start: 0.7264 (t0) cc_final: 0.6860 (t70) REVERT: A 335 SER cc_start: 0.8101 (t) cc_final: 0.7853 (p) REVERT: A 353 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7820 (mp) REVERT: A 366 THR cc_start: 0.8597 (OUTLIER) cc_final: 0.8246 (t) REVERT: A 369 ASN cc_start: 0.7593 (m-40) cc_final: 0.7086 (m-40) REVERT: A 372 LYS cc_start: 0.7745 (mttm) cc_final: 0.7389 (mttm) REVERT: A 378 PHE cc_start: 0.7753 (m-80) cc_final: 0.7412 (m-80) REVERT: A 481 TYR cc_start: 0.8321 (t80) cc_final: 0.8003 (t80) REVERT: A 523 GLN cc_start: 0.7657 (tm-30) cc_final: 0.7329 (tm-30) outliers start: 24 outliers final: 17 residues processed: 186 average time/residue: 0.0900 time to fit residues: 20.6538 Evaluate side-chains 194 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 175 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 513 HIS Chi-restraints excluded: chain A residue 519 LYS Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 588 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 41 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 20 optimal weight: 0.1980 chunk 49 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 ASN A 369 ASN A 434 ASN A 513 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.158328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.128800 restraints weight = 8954.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.132267 restraints weight = 4357.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.134465 restraints weight = 2562.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.135960 restraints weight = 1744.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.136577 restraints weight = 1325.926| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6206 Z= 0.163 Angle : 0.562 8.031 8530 Z= 0.325 Chirality : 0.044 0.161 957 Planarity : 0.004 0.060 950 Dihedral : 20.674 135.591 1100 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.08 % Favored : 97.76 % Rotamer: Outliers : 4.24 % Allowed : 19.32 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.75 (0.35), residues: 625 helix: 1.28 (0.30), residues: 304 sheet: -0.80 (0.57), residues: 76 loop : 0.10 (0.44), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 214 TYR 0.007 0.001 TYR A 42 PHE 0.013 0.001 PHE A 58 TRP 0.014 0.002 TRP A 512 HIS 0.004 0.001 HIS A 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 ( 6206) covalent geometry : angle 0.56155 / 0.32 ( 8530) hydrogen bonds : bond 0.04591 / 2.78 ( 306) hydrogen bonds : angle 4.72614 / 3.27 ( 836) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 181 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.8225 (tttp) cc_final: 0.7951 (tttp) REVERT: A 48 LYS cc_start: 0.8417 (tttt) cc_final: 0.8110 (tptt) REVERT: A 68 ASN cc_start: 0.7945 (m-40) cc_final: 0.7741 (m-40) REVERT: A 78 TYR cc_start: 0.7985 (p90) cc_final: 0.7336 (p90) REVERT: A 93 GLU cc_start: 0.6845 (mm-30) cc_final: 0.6504 (mm-30) REVERT: A 117 LYS cc_start: 0.7302 (mmtm) cc_final: 0.6983 (mmtm) REVERT: A 170 ASN cc_start: 0.6742 (t0) cc_final: 0.6216 (t0) REVERT: A 200 ASN cc_start: 0.7861 (t0) cc_final: 0.7639 (t0) REVERT: A 210 PHE cc_start: 0.6875 (m-80) cc_final: 0.6579 (m-80) REVERT: A 221 LYS cc_start: 0.7507 (mmmm) cc_final: 0.7152 (mmtp) REVERT: A 251 ASP cc_start: 0.7671 (t0) cc_final: 0.7277 (t70) REVERT: A 284 LYS cc_start: 0.7812 (mmmm) cc_final: 0.7457 (mmmm) REVERT: A 321 ASP cc_start: 0.7268 (t0) cc_final: 0.6757 (t70) REVERT: A 335 SER cc_start: 0.8089 (t) cc_final: 0.7819 (p) REVERT: A 353 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7802 (mp) REVERT: A 366 THR cc_start: 0.8585 (OUTLIER) cc_final: 0.8246 (t) REVERT: A 369 ASN cc_start: 0.7491 (m110) cc_final: 0.7045 (m110) REVERT: A 372 LYS cc_start: 0.7749 (mttm) cc_final: 0.7374 (mttm) REVERT: A 378 PHE cc_start: 0.7756 (m-80) cc_final: 0.7407 (m-80) REVERT: A 481 TYR cc_start: 0.8310 (t80) cc_final: 0.7968 (t80) REVERT: A 490 MET cc_start: 0.6086 (OUTLIER) cc_final: 0.5861 (tmm) REVERT: A 523 GLN cc_start: 0.7652 (tm-30) cc_final: 0.7325 (tm-30) outliers start: 25 outliers final: 17 residues processed: 187 average time/residue: 0.0973 time to fit residues: 22.5709 Evaluate side-chains 197 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 177 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 490 MET Chi-restraints excluded: chain A residue 519 LYS Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 602 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 36 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 7 optimal weight: 0.3980 chunk 3 optimal weight: 8.9990 chunk 53 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 466 ASN A 513 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.157425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.128047 restraints weight = 9067.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.131533 restraints weight = 4405.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.133809 restraints weight = 2579.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.135223 restraints weight = 1741.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.136153 restraints weight = 1326.890| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6206 Z= 0.164 Angle : 0.564 9.018 8530 Z= 0.324 Chirality : 0.044 0.164 957 Planarity : 0.004 0.061 950 Dihedral : 20.657 135.574 1100 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.24 % Favored : 97.60 % Rotamer: Outliers : 4.41 % Allowed : 18.98 % Favored : 76.61 % 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 are not related in a simple way. whole: 0.76 (0.35), residues: 625 helix: 1.29 (0.30), residues: 304 sheet: -0.78 (0.57), residues: 76 loop : 0.10 (0.44), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 337 TYR 0.009 0.001 TYR A 471 PHE 0.028 0.002 PHE A 406 TRP 0.006 0.001 TRP A 199 HIS 0.004 0.001 HIS A 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 ( 6206) covalent geometry : angle 0.56402 / 0.32 ( 8530) hydrogen bonds : bond 0.04451 / 2.70 ( 306) hydrogen bonds : angle 4.66235 / 3.22 ( 836) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 172 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.8224 (tttp) cc_final: 0.7986 (tttp) REVERT: A 27 LYS cc_start: 0.7284 (mtmt) cc_final: 0.6865 (mmmt) REVERT: A 48 LYS cc_start: 0.8371 (tttt) cc_final: 0.8092 (tptt) REVERT: A 78 TYR cc_start: 0.7968 (p90) cc_final: 0.7250 (p90) REVERT: A 93 GLU cc_start: 0.6888 (mm-30) cc_final: 0.6507 (mm-30) REVERT: A 117 LYS cc_start: 0.7294 (mmtm) cc_final: 0.6995 (mmtm) REVERT: A 170 ASN cc_start: 0.6737 (t0) cc_final: 0.6207 (t0) REVERT: A 200 ASN cc_start: 0.7860 (t0) cc_final: 0.7633 (t0) REVERT: A 210 PHE cc_start: 0.6885 (m-80) cc_final: 0.6556 (m-80) REVERT: A 221 LYS cc_start: 0.7511 (mmmm) cc_final: 0.7158 (mmtp) REVERT: A 251 ASP cc_start: 0.7713 (t0) cc_final: 0.7283 (t70) REVERT: A 284 LYS cc_start: 0.7826 (mmmm) cc_final: 0.7461 (mmmm) REVERT: A 321 ASP cc_start: 0.7217 (t0) cc_final: 0.6864 (t70) REVERT: A 335 SER cc_start: 0.8130 (t) cc_final: 0.7858 (p) REVERT: A 353 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7794 (mp) REVERT: A 366 THR cc_start: 0.8548 (OUTLIER) cc_final: 0.8208 (t) REVERT: A 369 ASN cc_start: 0.7486 (m110) cc_final: 0.7055 (m110) REVERT: A 372 LYS cc_start: 0.7750 (mttm) cc_final: 0.7379 (mttm) REVERT: A 481 TYR cc_start: 0.8280 (t80) cc_final: 0.7966 (t80) REVERT: A 523 GLN cc_start: 0.7640 (tm-30) cc_final: 0.7306 (tm-30) outliers start: 26 outliers final: 19 residues processed: 180 average time/residue: 0.0968 time to fit residues: 21.7771 Evaluate side-chains 191 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 170 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 296 GLN Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 519 LYS Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 602 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 47 optimal weight: 2.9990 chunk 32 optimal weight: 0.0980 chunk 34 optimal weight: 0.6980 chunk 64 optimal weight: 9.9990 chunk 19 optimal weight: 0.3980 chunk 4 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 513 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.158238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.128780 restraints weight = 9020.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.132268 restraints weight = 4406.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.134430 restraints weight = 2596.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.135969 restraints weight = 1770.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.136779 restraints weight = 1340.499| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6206 Z= 0.148 Angle : 0.562 10.206 8530 Z= 0.322 Chirality : 0.044 0.158 957 Planarity : 0.003 0.060 950 Dihedral : 20.585 135.667 1100 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.92 % Favored : 97.92 % Rotamer: Outliers : 4.58 % Allowed : 18.98 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.79 (0.35), residues: 625 helix: 1.31 (0.30), residues: 304 sheet: -0.73 (0.57), residues: 76 loop : 0.09 (0.43), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 337 TYR 0.013 0.001 TYR A 471 PHE 0.025 0.002 PHE A 406 TRP 0.005 0.001 TRP A 624 HIS 0.004 0.001 HIS A 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 ( 6206) covalent geometry : angle 0.56233 / 0.32 ( 8530) hydrogen bonds : bond 0.04216 / 2.55 ( 306) hydrogen bonds : angle 4.63888 / 3.22 ( 836) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 170 time to evaluate : 0.168 Fit side-chains revert: symmetry clash REVERT: A 21 LYS cc_start: 0.8204 (tttp) cc_final: 0.7998 (tttp) REVERT: A 27 LYS cc_start: 0.7268 (mtmt) cc_final: 0.6867 (mmmt) REVERT: A 48 LYS cc_start: 0.8333 (tttt) cc_final: 0.8066 (tptt) REVERT: A 78 TYR cc_start: 0.7926 (p90) cc_final: 0.7232 (p90) REVERT: A 84 GLN cc_start: 0.7587 (mm-40) cc_final: 0.7327 (mm-40) REVERT: A 117 LYS cc_start: 0.7256 (mmtm) cc_final: 0.6992 (mmtm) REVERT: A 170 ASN cc_start: 0.6694 (t0) cc_final: 0.6179 (t0) REVERT: A 200 ASN cc_start: 0.7841 (t0) cc_final: 0.7616 (t0) REVERT: A 210 PHE cc_start: 0.6865 (m-80) cc_final: 0.6576 (m-80) REVERT: A 251 ASP cc_start: 0.7698 (t0) cc_final: 0.7160 (t70) REVERT: A 253 GLU cc_start: 0.7501 (mt-10) cc_final: 0.7182 (mt-10) REVERT: A 271 ILE cc_start: 0.7041 (OUTLIER) cc_final: 0.6793 (tp) REVERT: A 284 LYS cc_start: 0.7808 (mmmm) cc_final: 0.7455 (mmmm) REVERT: A 321 ASP cc_start: 0.7163 (t0) cc_final: 0.6932 (t0) REVERT: A 335 SER cc_start: 0.8043 (t) cc_final: 0.7781 (p) REVERT: A 353 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7791 (mp) REVERT: A 366 THR cc_start: 0.8547 (OUTLIER) cc_final: 0.8174 (t) REVERT: A 369 ASN cc_start: 0.7493 (m110) cc_final: 0.7050 (m110) REVERT: A 372 LYS cc_start: 0.7746 (mttm) cc_final: 0.7361 (mttm) REVERT: A 481 TYR cc_start: 0.8252 (t80) cc_final: 0.7948 (t80) REVERT: A 523 GLN cc_start: 0.7622 (tm-30) cc_final: 0.7309 (tm-30) outliers start: 27 outliers final: 20 residues processed: 180 average time/residue: 0.0940 time to fit residues: 21.1059 Evaluate side-chains 192 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 169 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 296 GLN Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 513 HIS Chi-restraints excluded: chain A residue 519 LYS Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 602 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 40 optimal weight: 0.5980 chunk 37 optimal weight: 0.0050 chunk 27 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 65 optimal weight: 20.0000 chunk 14 optimal weight: 0.0570 chunk 32 optimal weight: 3.9990 overall best weight: 0.4512 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 172 ASN A 466 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.157567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.127919 restraints weight = 9026.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.131410 restraints weight = 4401.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.133649 restraints weight = 2586.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.135155 restraints weight = 1760.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.136043 restraints weight = 1333.940| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6206 Z= 0.148 Angle : 0.588 12.101 8530 Z= 0.330 Chirality : 0.044 0.164 957 Planarity : 0.004 0.060 950 Dihedral : 20.520 135.783 1100 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.40 % Favored : 97.44 % Rotamer: Outliers : 4.41 % Allowed : 19.32 % Favored : 76.27 % 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 are not related in a simple way. whole: 0.78 (0.35), residues: 625 helix: 1.30 (0.30), residues: 305 sheet: -0.68 (0.57), residues: 76 loop : 0.08 (0.43), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 341 TYR 0.012 0.001 TYR A 471 PHE 0.023 0.002 PHE A 406 TRP 0.005 0.001 TRP A 199 HIS 0.013 0.002 HIS A 513 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 ( 6206) covalent geometry : angle 0.58826 / 0.33 ( 8530) hydrogen bonds : bond 0.04175 / 2.52 ( 306) hydrogen bonds : angle 4.58411 / 3.18 ( 836) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 170 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: A 21 LYS cc_start: 0.8226 (tttp) cc_final: 0.8021 (tttp) REVERT: A 48 LYS cc_start: 0.8352 (tttt) cc_final: 0.8071 (tptt) REVERT: A 78 TYR cc_start: 0.7931 (p90) cc_final: 0.7172 (p90) REVERT: A 117 LYS cc_start: 0.7268 (mmtm) cc_final: 0.6998 (mmtm) REVERT: A 170 ASN cc_start: 0.6709 (t0) cc_final: 0.6182 (t0) REVERT: A 200 ASN cc_start: 0.7857 (t0) cc_final: 0.7622 (t0) REVERT: A 210 PHE cc_start: 0.6848 (m-80) cc_final: 0.6548 (m-80) REVERT: A 251 ASP cc_start: 0.7693 (t0) cc_final: 0.7148 (t70) REVERT: A 253 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7189 (mt-10) REVERT: A 271 ILE cc_start: 0.7012 (OUTLIER) cc_final: 0.6737 (tp) REVERT: A 284 LYS cc_start: 0.7824 (mmmm) cc_final: 0.7466 (mmmm) REVERT: A 335 SER cc_start: 0.8048 (t) cc_final: 0.7799 (p) REVERT: A 353 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7755 (mp) REVERT: A 366 THR cc_start: 0.8525 (OUTLIER) cc_final: 0.8178 (t) REVERT: A 369 ASN cc_start: 0.7496 (m110) cc_final: 0.7041 (m110) REVERT: A 372 LYS cc_start: 0.7757 (mttm) cc_final: 0.7358 (mttm) REVERT: A 481 TYR cc_start: 0.8248 (t80) cc_final: 0.7930 (t80) REVERT: A 523 GLN cc_start: 0.7623 (tm-30) cc_final: 0.7297 (tm-30) outliers start: 26 outliers final: 18 residues processed: 176 average time/residue: 0.0845 time to fit residues: 18.6262 Evaluate side-chains 190 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 169 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 519 LYS Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 602 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 22 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 3 optimal weight: 9.9990 chunk 14 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 172 ASN A 466 ASN A 513 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.156292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.126646 restraints weight = 8991.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.130092 restraints weight = 4455.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.132341 restraints weight = 2640.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.133799 restraints weight = 1798.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.134756 restraints weight = 1367.988| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6206 Z= 0.191 Angle : 0.610 12.964 8530 Z= 0.339 Chirality : 0.045 0.160 957 Planarity : 0.003 0.062 950 Dihedral : 20.441 135.753 1100 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.56 % Favored : 97.28 % Rotamer: Outliers : 3.90 % Allowed : 20.34 % Favored : 75.76 % 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 are not related in a simple way. whole: 0.73 (0.35), residues: 625 helix: 1.27 (0.30), residues: 304 sheet: -0.68 (0.57), residues: 76 loop : 0.03 (0.43), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 341 TYR 0.010 0.001 TYR A 42 PHE 0.026 0.002 PHE A 406 TRP 0.006 0.002 TRP A 199 HIS 0.004 0.001 HIS A 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.19 ( 6206) covalent geometry : angle 0.61016 / 0.34 ( 8530) hydrogen bonds : bond 0.04500 / 2.73 ( 306) hydrogen bonds : angle 4.60159 / 3.18 ( 836) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 175 time to evaluate : 0.196 Fit side-chains revert: symmetry clash REVERT: A 13 ILE cc_start: 0.8284 (OUTLIER) cc_final: 0.7885 (pt) REVERT: A 21 LYS cc_start: 0.8240 (tttp) cc_final: 0.8030 (tttp) REVERT: A 48 LYS cc_start: 0.8356 (tttt) cc_final: 0.8061 (tptt) REVERT: A 78 TYR cc_start: 0.7937 (p90) cc_final: 0.7222 (p90) REVERT: A 84 GLN cc_start: 0.7605 (mm-40) cc_final: 0.7370 (mm-40) REVERT: A 93 GLU cc_start: 0.6948 (mm-30) cc_final: 0.6552 (mm-30) REVERT: A 117 LYS cc_start: 0.7267 (mmtm) cc_final: 0.6982 (mmtm) REVERT: A 170 ASN cc_start: 0.6719 (t0) cc_final: 0.6189 (t0) REVERT: A 200 ASN cc_start: 0.7889 (t0) cc_final: 0.7643 (t0) REVERT: A 210 PHE cc_start: 0.6862 (m-80) cc_final: 0.6623 (m-80) REVERT: A 221 LYS cc_start: 0.7486 (mmmm) cc_final: 0.7096 (mttm) REVERT: A 251 ASP cc_start: 0.7701 (t0) cc_final: 0.7173 (t70) REVERT: A 253 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7152 (mt-10) REVERT: A 271 ILE cc_start: 0.7013 (OUTLIER) cc_final: 0.6780 (tp) REVERT: A 284 LYS cc_start: 0.7830 (mmmm) cc_final: 0.7472 (mmmm) REVERT: A 335 SER cc_start: 0.8086 (t) cc_final: 0.7777 (p) REVERT: A 353 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7797 (mp) REVERT: A 366 THR cc_start: 0.8554 (OUTLIER) cc_final: 0.8248 (t) REVERT: A 369 ASN cc_start: 0.7484 (m110) cc_final: 0.7046 (m110) REVERT: A 372 LYS cc_start: 0.7761 (mttm) cc_final: 0.7368 (mttm) REVERT: A 481 TYR cc_start: 0.8261 (t80) cc_final: 0.7958 (t80) outliers start: 23 outliers final: 15 residues processed: 182 average time/residue: 0.0832 time to fit residues: 19.1014 Evaluate side-chains 184 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 165 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 296 GLN Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 490 MET Chi-restraints excluded: chain A residue 513 HIS Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 588 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 63 optimal weight: 10.0000 chunk 31 optimal weight: 0.1980 chunk 62 optimal weight: 20.0000 chunk 17 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 19 optimal weight: 0.0970 chunk 49 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 172 ASN A 466 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.158225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.128485 restraints weight = 8998.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.131946 restraints weight = 4445.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.134205 restraints weight = 2630.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.135669 restraints weight = 1801.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.136532 restraints weight = 1371.985| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6206 Z= 0.153 Angle : 0.606 13.206 8530 Z= 0.336 Chirality : 0.044 0.158 957 Planarity : 0.004 0.059 950 Dihedral : 20.410 135.536 1100 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.24 % Favored : 97.60 % Rotamer: Outliers : 3.56 % Allowed : 20.51 % Favored : 75.93 % 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 are not related in a simple way. whole: 0.75 (0.35), residues: 625 helix: 1.30 (0.30), residues: 305 sheet: -0.67 (0.57), residues: 76 loop : 0.01 (0.43), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 459 TYR 0.023 0.001 TYR A 471 PHE 0.024 0.002 PHE A 406 TRP 0.017 0.002 TRP A 512 HIS 0.007 0.001 HIS A 513 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 ( 6206) covalent geometry : angle 0.60604 / 0.34 ( 8530) hydrogen bonds : bond 0.04239 / 2.57 ( 306) hydrogen bonds : angle 4.54946 / 3.15 ( 836) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1119.56 seconds wall clock time: 20 minutes 4.61 seconds (1204.61 seconds total)