Starting phenix.real_space_refine on Tue Aug 4 18:56:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9quj_53378/08_2026/9quj_53378.cif Found real_map, /net/cci-nas-00/data/ceres_data/9quj_53378/08_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_53378/08_2026/9quj_53378.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9quj_53378/08_2026/9quj_53378.map" model { file = "/net/cci-nas-00/data/ceres_data/9quj_53378/08_2026/9quj_53378.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9quj_53378/08_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/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: 1.72, per 1000 atoms: 0.29 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: 0.64 Conformation dependent library (CDL) restraints added in 391.2 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: 0.82 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: 1.41 Time building geometry restraints manager: 0.81 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: 7944 1.16 - 2.32: 459 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: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.410 Find NCS groups from input model: 0.050 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.180 ------------------------------------------------------------------------------- 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 : 0.650 5.795 8530 Z= 0.487 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 0.65047 / 0.49 ( 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 : 0.126 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: 0.0811 time to fit residues: 20.2709 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 : 0.144 ------------------------------------------------------------------------------- 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 = 0.156482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.126489 restraints weight = 9004.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.129940 restraints weight = 4426.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.132125 restraints weight = 2621.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.133581 restraints weight = 1787.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.134384 restraints weight = 1368.761| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.1157 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= 0.199 Angle : 0.621 6.210 8530 Z= 0.363 Chirality : 0.047 0.201 957 Planarity : 0.004 0.053 950 Dihedral : 20.205 137.781 1100 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.04 % Favored : 96.80 % 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: 0.88 (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 0.006 0.001 ARG A 214 TYR 0.008 0.001 TYR A 499 PHE 0.016 0.002 PHE A 411 TRP 0.018 0.003 TRP A 624 HIS 0.003 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.20 ( 6206) covalent geometry : angle 0.62070 / 0.36 ( 8530) hydrogen bonds : bond 0.05718 / 3.50 ( 306) hydrogen bonds : angle 5.31005 / 3.68 ( 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 196 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 180 time to evaluate : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.8193 (tt) cc_final: 0.7779 (pt) REVERT: A 48 LYS cc_start: 0.8361 (tttt) cc_final: 0.8135 (tptt) REVERT: A 68 ASN cc_start: 0.7982 (m-40) cc_final: 0.7770 (m-40) REVERT: A 78 TYR cc_start: 0.8001 (p90) cc_final: 0.7571 (p90) REVERT: A 103 GLU cc_start: 0.7762 (tt0) cc_final: 0.7434 (tt0) REVERT: A 168 ASP cc_start: 0.6553 (OUTLIER) cc_final: 0.6299 (m-30) REVERT: A 170 ASN cc_start: 0.6785 (t0) cc_final: 0.6451 (t0) REVERT: A 200 ASN cc_start: 0.7888 (t0) cc_final: 0.7652 (t0) REVERT: A 210 PHE cc_start: 0.6862 (m-80) cc_final: 0.6555 (m-80) REVERT: A 251 ASP cc_start: 0.7744 (t70) cc_final: 0.7415 (t70) REVERT: A 253 GLU cc_start: 0.7484 (mt-10) cc_final: 0.6964 (mt-10) REVERT: A 287 LYS cc_start: 0.8404 (mmmt) cc_final: 0.7936 (mmmt) REVERT: A 335 SER cc_start: 0.8144 (t) cc_final: 0.7887 (p) REVERT: A 341 ARG cc_start: 0.7866 (ttp80) cc_final: 0.7665 (ttp80) REVERT: A 369 ASN cc_start: 0.7724 (m-40) cc_final: 0.7304 (m-40) REVERT: A 372 LYS cc_start: 0.7714 (mttm) cc_final: 0.7353 (mttm) REVERT: A 378 PHE cc_start: 0.7694 (m-80) cc_final: 0.7349 (m-80) REVERT: A 481 TYR cc_start: 0.8308 (t80) cc_final: 0.8032 (t80) REVERT: A 510 TYR cc_start: 0.7436 (t80) cc_final: 0.6967 (t80) REVERT: A 514 ASN cc_start: 0.7744 (m-40) cc_final: 0.7440 (m-40) REVERT: A 523 GLN cc_start: 0.7716 (tm-30) cc_final: 0.7332 (tm-30) outliers start: 16 outliers final: 10 residues processed: 186 average time/residue: 0.0805 time to fit residues: 18.4520 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 : 0.125 ------------------------------------------------------------------------------- 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: 3.9990 chunk 59 optimal weight: 0.0980 chunk 25 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 63 optimal weight: 10.0000 chunk 58 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 37 optimal weight: 0.4980 chunk 54 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3992 r_free = 0.3992 target = 0.158502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.128276 restraints weight = 9102.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.131836 restraints weight = 4428.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.134096 restraints weight = 2603.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.135567 restraints weight = 1762.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.136510 restraints weight = 1341.938| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6206 Z= 0.160 Angle : 0.569 5.899 8530 Z= 0.335 Chirality : 0.045 0.174 957 Planarity : 0.004 0.056 950 Dihedral : 20.443 136.561 1100 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.40 % Favored : 97.44 % Rotamer: Outliers : 4.92 % Allowed : 13.22 % Favored : 81.86 % 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: 0.42 (0.35), residues: 625 helix: 0.96 (0.29), residues: 309 sheet: -0.73 (0.59), residues: 76 loop : -0.11 (0.44), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 459 TYR 0.009 0.001 TYR A 471 PHE 0.013 0.002 PHE A 210 TRP 0.013 0.003 TRP A 624 HIS 0.003 0.001 HIS A 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.16 ( 6206) covalent geometry : angle 0.56856 / 0.33 ( 8530) hydrogen bonds : bond 0.05102 / 3.09 ( 306) hydrogen bonds : angle 5.00374 / 3.47 ( 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 205 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 176 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.8189 (tt) cc_final: 0.7821 (pt) REVERT: A 21 LYS cc_start: 0.8135 (tttp) cc_final: 0.7858 (tttp) REVERT: A 48 LYS cc_start: 0.8403 (tttt) cc_final: 0.8155 (tptt) REVERT: A 68 ASN cc_start: 0.7978 (m-40) cc_final: 0.7745 (m-40) REVERT: A 78 TYR cc_start: 0.7981 (p90) cc_final: 0.7521 (p90) REVERT: A 84 GLN cc_start: 0.7519 (mm-40) cc_final: 0.7274 (mm-40) REVERT: A 103 GLU cc_start: 0.7740 (tt0) cc_final: 0.7415 (tt0) REVERT: A 170 ASN cc_start: 0.6754 (t0) cc_final: 0.6429 (t0) REVERT: A 200 ASN cc_start: 0.7877 (t0) cc_final: 0.7611 (t0) REVERT: A 210 PHE cc_start: 0.6882 (m-80) cc_final: 0.6565 (m-80) REVERT: A 335 SER cc_start: 0.8087 (t) cc_final: 0.7853 (p) REVERT: A 341 ARG cc_start: 0.7861 (ttp80) cc_final: 0.7654 (ttp80) REVERT: A 353 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7822 (mp) REVERT: A 366 THR cc_start: 0.8625 (OUTLIER) cc_final: 0.8221 (t) REVERT: A 369 ASN cc_start: 0.7717 (m-40) cc_final: 0.7175 (m-40) REVERT: A 372 LYS cc_start: 0.7759 (mttm) cc_final: 0.7360 (mttm) REVERT: A 378 PHE cc_start: 0.7711 (m-80) cc_final: 0.7355 (m-80) REVERT: A 387 GLN cc_start: 0.7223 (OUTLIER) cc_final: 0.7018 (tp-100) REVERT: A 481 TYR cc_start: 0.8290 (t80) cc_final: 0.8005 (t80) REVERT: A 523 GLN cc_start: 0.7689 (tm-30) cc_final: 0.7335 (tm-30) outliers start: 29 outliers final: 16 residues processed: 186 average time/residue: 0.0808 time to fit residues: 18.6864 Evaluate side-chains 191 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 172 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LYS 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 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 387 GLN Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 519 LYS Chi-restraints excluded: chain A residue 543 LEU 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: 2.9990 chunk 34 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 35 optimal weight: 0.3980 chunk 53 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3976 r_free = 0.3976 target = 0.157168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.127183 restraints weight = 9016.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.130677 restraints weight = 4426.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.132909 restraints weight = 2607.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.134350 restraints weight = 1770.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.135200 restraints weight = 1352.761| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 6206 Z= 0.222 Angle : 0.588 6.050 8530 Z= 0.341 Chirality : 0.046 0.168 957 Planarity : 0.004 0.064 950 Dihedral : 20.611 135.957 1100 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.56 % Favored : 97.28 % Rotamer: Outliers : 3.56 % Allowed : 17.46 % Favored : 78.98 % 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: 0.43 (0.35), residues: 625 helix: 0.99 (0.30), residues: 308 sheet: -0.75 (0.58), residues: 76 loop : -0.13 (0.44), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 337 TYR 0.013 0.001 TYR A 73 PHE 0.014 0.002 PHE A 58 TRP 0.008 0.002 TRP A 624 HIS 0.005 0.001 HIS A 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.22 ( 6206) covalent geometry : angle 0.58835 / 0.34 ( 8530) hydrogen bonds : bond 0.05236 / 3.18 ( 306) hydrogen bonds : angle 4.94298 / 3.42 ( 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 207 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 186 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.8222 (tt) cc_final: 0.7828 (pt) REVERT: A 21 LYS cc_start: 0.8127 (tttp) cc_final: 0.7836 (tttp) REVERT: A 48 LYS cc_start: 0.8419 (tttt) cc_final: 0.8125 (tptt) REVERT: A 68 ASN cc_start: 0.7977 (m-40) cc_final: 0.7730 (m-40) REVERT: A 78 TYR cc_start: 0.8001 (p90) cc_final: 0.7416 (p90) REVERT: A 117 LYS cc_start: 0.7321 (mmtm) cc_final: 0.7017 (mmtm) REVERT: A 170 ASN cc_start: 0.6756 (t0) cc_final: 0.6410 (t0) REVERT: A 200 ASN cc_start: 0.7884 (t0) cc_final: 0.7619 (t0) REVERT: A 210 PHE cc_start: 0.6900 (m-80) cc_final: 0.6604 (m-80) REVERT: A 251 ASP cc_start: 0.7684 (t0) cc_final: 0.7342 (t70) REVERT: A 284 LYS cc_start: 0.7831 (mmmm) cc_final: 0.7448 (mmmm) REVERT: A 321 ASP cc_start: 0.7294 (t0) cc_final: 0.6829 (t70) REVERT: A 335 SER cc_start: 0.8123 (t) cc_final: 0.7872 (p) REVERT: A 369 ASN cc_start: 0.7608 (m-40) cc_final: 0.7105 (m-40) REVERT: A 372 LYS cc_start: 0.7738 (mttm) cc_final: 0.7383 (mttm) REVERT: A 378 PHE cc_start: 0.7742 (m-80) cc_final: 0.7351 (m-80) REVERT: A 387 GLN cc_start: 0.7178 (OUTLIER) cc_final: 0.6972 (tp-100) REVERT: A 481 TYR cc_start: 0.8342 (t80) cc_final: 0.8030 (t80) REVERT: A 490 MET cc_start: 0.5931 (tmm) cc_final: 0.5698 (ttm) REVERT: A 523 GLN cc_start: 0.7677 (tm-30) cc_final: 0.7287 (tm-30) outliers start: 21 outliers final: 15 residues processed: 192 average time/residue: 0.1056 time to fit residues: 25.2293 Evaluate side-chains 192 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 176 time to evaluate : 0.216 ------------------------------------------------------------------------------- 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 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 332 GLU Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 387 GLN Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 513 HIS 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: 2.9990 chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 57 optimal weight: 0.0570 chunk 45 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 ASN ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 369 ASN A 370 GLN 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 = 0.158403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.128643 restraints weight = 9121.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.132176 restraints weight = 4425.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.134411 restraints weight = 2593.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.135881 restraints weight = 1758.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.136816 restraints weight = 1328.177| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.1829 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= 0.167 Angle : 0.567 7.335 8530 Z= 0.328 Chirality : 0.045 0.155 957 Planarity : 0.004 0.060 950 Dihedral : 20.653 135.548 1100 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.08 % Favored : 97.76 % Rotamer: Outliers : 3.90 % Allowed : 19.15 % Favored : 76.95 % 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: 0.48 (0.35), residues: 625 helix: 1.02 (0.30), residues: 309 sheet: -0.80 (0.57), residues: 76 loop : -0.06 (0.44), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 459 TYR 0.008 0.001 TYR A 42 PHE 0.013 0.002 PHE A 58 TRP 0.006 0.002 TRP A 199 HIS 0.008 0.001 HIS A 513 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.17 ( 6206) covalent geometry : angle 0.56661 / 0.33 ( 8530) hydrogen bonds : bond 0.04776 / 2.89 ( 306) hydrogen bonds : angle 4.85071 / 3.37 ( 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 205 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 182 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.8167 (tttp) cc_final: 0.7850 (tttp) REVERT: A 48 LYS cc_start: 0.8411 (tttt) cc_final: 0.8140 (tptt) REVERT: A 68 ASN cc_start: 0.7957 (m-40) cc_final: 0.7752 (m-40) REVERT: A 78 TYR cc_start: 0.7973 (p90) cc_final: 0.7319 (p90) REVERT: A 93 GLU cc_start: 0.6868 (mm-30) cc_final: 0.6529 (mm-30) REVERT: A 117 LYS cc_start: 0.7287 (mmtm) cc_final: 0.6970 (mmtm) REVERT: A 170 ASN cc_start: 0.6748 (t0) cc_final: 0.6201 (t0) REVERT: A 200 ASN cc_start: 0.7870 (t0) cc_final: 0.7641 (t0) REVERT: A 210 PHE cc_start: 0.6882 (m-80) cc_final: 0.6539 (m-80) REVERT: A 214 ARG cc_start: 0.7820 (mtp85) cc_final: 0.7517 (mtp85) REVERT: A 251 ASP cc_start: 0.7655 (t0) cc_final: 0.7335 (t70) REVERT: A 284 LYS cc_start: 0.7839 (mmmm) cc_final: 0.7460 (mmmm) REVERT: A 321 ASP cc_start: 0.7250 (t0) cc_final: 0.6641 (t70) REVERT: A 335 SER cc_start: 0.8127 (t) cc_final: 0.7864 (p) REVERT: A 366 THR cc_start: 0.8543 (OUTLIER) cc_final: 0.8132 (t) REVERT: A 369 ASN cc_start: 0.7466 (m110) cc_final: 0.7068 (m110) REVERT: A 372 LYS cc_start: 0.7740 (mttm) cc_final: 0.7381 (mttm) REVERT: A 378 PHE cc_start: 0.7731 (m-80) cc_final: 0.7380 (m-80) REVERT: A 481 TYR cc_start: 0.8341 (t80) cc_final: 0.8047 (t80) REVERT: A 523 GLN cc_start: 0.7662 (tm-30) cc_final: 0.7304 (tm-30) outliers start: 23 outliers final: 16 residues processed: 189 average time/residue: 0.1065 time to fit residues: 24.9306 Evaluate side-chains 196 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 179 time to evaluate : 0.212 ------------------------------------------------------------------------------- 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 436 ILE 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: 0.9990 chunk 40 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3983 r_free = 0.3983 target = 0.157950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.128214 restraints weight = 8967.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.131661 restraints weight = 4377.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.133940 restraints weight = 2581.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.135299 restraints weight = 1742.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.136291 restraints weight = 1336.776| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.1953 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= 0.180 Angle : 0.567 8.343 8530 Z= 0.328 Chirality : 0.044 0.159 957 Planarity : 0.004 0.061 950 Dihedral : 20.673 135.480 1100 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.08 % Favored : 97.76 % Rotamer: Outliers : 4.75 % Allowed : 18.81 % 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: 0.66 (0.35), residues: 625 helix: 1.16 (0.30), residues: 304 sheet: -0.79 (0.57), residues: 76 loop : 0.10 (0.44), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 337 TYR 0.009 0.001 TYR A 42 PHE 0.013 0.002 PHE A 58 TRP 0.007 0.002 TRP A 199 HIS 0.009 0.002 HIS A 513 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.18 ( 6206) covalent geometry : angle 0.56670 / 0.33 ( 8530) hydrogen bonds : bond 0.04714 / 2.86 ( 306) hydrogen bonds : angle 4.80522 / 3.33 ( 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 211 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 183 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.8166 (tttp) cc_final: 0.7882 (tttp) REVERT: A 48 LYS cc_start: 0.8381 (tttt) cc_final: 0.8129 (tptt) REVERT: A 68 ASN cc_start: 0.7964 (m-40) cc_final: 0.7751 (m-40) REVERT: A 78 TYR cc_start: 0.7999 (p90) cc_final: 0.7321 (p90) REVERT: A 117 LYS cc_start: 0.7309 (mmtm) cc_final: 0.6995 (mmtm) REVERT: A 170 ASN cc_start: 0.6755 (t0) cc_final: 0.6202 (t0) REVERT: A 200 ASN cc_start: 0.7863 (t0) cc_final: 0.7647 (t0) REVERT: A 210 PHE cc_start: 0.6878 (m-80) cc_final: 0.6579 (m-80) REVERT: A 214 ARG cc_start: 0.7839 (mtp85) cc_final: 0.7532 (mtp85) REVERT: A 251 ASP cc_start: 0.7681 (t0) cc_final: 0.7316 (t70) REVERT: A 284 LYS cc_start: 0.7849 (mmmm) cc_final: 0.7478 (mmmm) REVERT: A 321 ASP cc_start: 0.7232 (t0) cc_final: 0.6748 (t70) REVERT: A 335 SER cc_start: 0.8101 (t) cc_final: 0.7827 (p) REVERT: A 366 THR cc_start: 0.8555 (OUTLIER) cc_final: 0.8172 (t) REVERT: A 369 ASN cc_start: 0.7475 (m110) cc_final: 0.7085 (m110) REVERT: A 372 LYS cc_start: 0.7751 (mttm) cc_final: 0.7376 (mttm) REVERT: A 378 PHE cc_start: 0.7736 (m-80) cc_final: 0.7369 (m-80) REVERT: A 481 TYR cc_start: 0.8327 (t80) cc_final: 0.8012 (t80) REVERT: A 523 GLN cc_start: 0.7650 (tm-30) cc_final: 0.7322 (tm-30) outliers start: 28 outliers final: 23 residues processed: 192 average time/residue: 0.1086 time to fit residues: 26.0025 Evaluate side-chains 204 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 180 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 13 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 272 LEU Chi-restraints excluded: chain A residue 296 GLN 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 488 LEU 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 36 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 59 optimal weight: 0.3980 chunk 39 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 7 optimal weight: 0.3980 chunk 3 optimal weight: 10.0000 chunk 53 optimal weight: 0.3980 chunk 52 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3995 r_free = 0.3995 target = 0.158720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.128919 restraints weight = 9075.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.132452 restraints weight = 4438.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.134737 restraints weight = 2608.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.136233 restraints weight = 1766.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.137154 restraints weight = 1338.809| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6206 Z= 0.149 Angle : 0.559 9.343 8530 Z= 0.323 Chirality : 0.044 0.160 957 Planarity : 0.004 0.060 950 Dihedral : 20.642 135.473 1100 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.92 % Favored : 97.92 % Rotamer: Outliers : 4.24 % Allowed : 19.66 % Favored : 76.10 % 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: 1.22 (0.30), residues: 305 sheet: -0.77 (0.56), residues: 76 loop : 0.12 (0.44), residues: 244 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 0.013 0.001 PHE A 58 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 0.00306 / 0.15 ( 6206) covalent geometry : angle 0.55944 / 0.32 ( 8530) hydrogen bonds : bond 0.04413 / 2.69 ( 306) hydrogen bonds : angle 4.72400 / 3.28 ( 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 204 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 179 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.8192 (tttp) cc_final: 0.7909 (tttp) REVERT: A 48 LYS cc_start: 0.8382 (tttt) cc_final: 0.8101 (tptt) REVERT: A 78 TYR cc_start: 0.7973 (p90) cc_final: 0.7317 (p90) REVERT: A 84 GLN cc_start: 0.7549 (mm-40) cc_final: 0.7295 (mm-40) REVERT: A 117 LYS cc_start: 0.7263 (mmtm) cc_final: 0.6995 (mmtm) REVERT: A 170 ASN cc_start: 0.6740 (t0) cc_final: 0.6197 (t0) REVERT: A 200 ASN cc_start: 0.7868 (t0) cc_final: 0.7640 (t0) REVERT: A 210 PHE cc_start: 0.6870 (m-80) cc_final: 0.6616 (m-80) REVERT: A 214 ARG cc_start: 0.7814 (mtp85) cc_final: 0.7495 (mtp85) REVERT: A 251 ASP cc_start: 0.7661 (t0) cc_final: 0.7300 (t70) REVERT: A 252 MET cc_start: 0.7228 (mtp) cc_final: 0.6983 (mtp) REVERT: A 284 LYS cc_start: 0.7841 (mmmm) cc_final: 0.7456 (mmmm) REVERT: A 321 ASP cc_start: 0.7169 (t0) cc_final: 0.6926 (t0) REVERT: A 335 SER cc_start: 0.8093 (t) cc_final: 0.7802 (p) REVERT: A 366 THR cc_start: 0.8545 (OUTLIER) cc_final: 0.8198 (t) REVERT: A 369 ASN cc_start: 0.7496 (m110) cc_final: 0.7023 (m110) REVERT: A 372 LYS cc_start: 0.7741 (mttm) cc_final: 0.7385 (mttm) REVERT: A 481 TYR cc_start: 0.8294 (t80) cc_final: 0.7994 (t80) REVERT: A 523 GLN cc_start: 0.7631 (tm-30) cc_final: 0.7317 (tm-30) outliers start: 25 outliers final: 22 residues processed: 186 average time/residue: 0.1042 time to fit residues: 24.2274 Evaluate side-chains 200 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 177 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 13 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 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 387 GLN Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 488 LEU 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 47 optimal weight: 0.0040 chunk 32 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 chunk 19 optimal weight: 0.1980 chunk 4 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 45 optimal weight: 0.0980 chunk 54 optimal weight: 0.4980 overall best weight: 0.3192 ------------------------------------------------------------------------------- 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 = 0.4000 r_free = 0.4000 target = 0.158382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.128581 restraints weight = 9010.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.132123 restraints weight = 4405.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.134431 restraints weight = 2589.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.135925 restraints weight = 1755.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.136749 restraints weight = 1333.189| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.2223 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= 0.137 Angle : 0.566 10.352 8530 Z= 0.324 Chirality : 0.044 0.161 957 Planarity : 0.004 0.060 950 Dihedral : 20.591 135.651 1100 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.76 % Favored : 98.08 % Rotamer: Outliers : 3.90 % Allowed : 19.83 % 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: 0.82 (0.35), residues: 625 helix: 1.33 (0.30), residues: 305 sheet: -0.74 (0.56), residues: 76 loop : 0.14 (0.43), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 337 TYR 0.011 0.001 TYR A 471 PHE 0.026 0.002 PHE A 406 TRP 0.005 0.001 TRP A 512 HIS 0.004 0.001 HIS A 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.14 ( 6206) covalent geometry : angle 0.56612 / 0.32 ( 8530) hydrogen bonds : bond 0.04179 / 2.54 ( 306) hydrogen bonds : angle 4.62408 / 3.21 ( 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 199 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 176 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.8212 (tttp) cc_final: 0.7929 (tttp) REVERT: A 27 LYS cc_start: 0.7261 (mtmt) cc_final: 0.6876 (mmmt) REVERT: A 48 LYS cc_start: 0.8318 (tttt) cc_final: 0.8047 (tptt) REVERT: A 78 TYR cc_start: 0.7930 (p90) cc_final: 0.7230 (p90) REVERT: A 84 GLN cc_start: 0.7566 (mm-40) cc_final: 0.7333 (mm-40) REVERT: A 117 LYS cc_start: 0.7207 (mmtm) cc_final: 0.6988 (mmtm) REVERT: A 170 ASN cc_start: 0.6702 (t0) cc_final: 0.6183 (t0) REVERT: A 200 ASN cc_start: 0.7852 (t0) cc_final: 0.7618 (t0) REVERT: A 210 PHE cc_start: 0.6870 (m-80) cc_final: 0.6601 (m-80) REVERT: A 251 ASP cc_start: 0.7662 (t0) cc_final: 0.7162 (t70) REVERT: A 253 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7260 (mt-10) REVERT: A 284 LYS cc_start: 0.7792 (mmmm) cc_final: 0.7441 (mmmm) REVERT: A 321 ASP cc_start: 0.7094 (t0) cc_final: 0.6867 (t0) REVERT: A 335 SER cc_start: 0.8074 (t) cc_final: 0.7731 (p) REVERT: A 366 THR cc_start: 0.8546 (OUTLIER) cc_final: 0.8080 (t) REVERT: A 369 ASN cc_start: 0.7483 (m110) cc_final: 0.7015 (m110) REVERT: A 372 LYS cc_start: 0.7737 (mttm) cc_final: 0.7370 (mttm) REVERT: A 481 TYR cc_start: 0.8237 (t80) cc_final: 0.7930 (t80) REVERT: A 523 GLN cc_start: 0.7611 (tm-30) cc_final: 0.7316 (tm-30) outliers start: 23 outliers final: 19 residues processed: 184 average time/residue: 0.1066 time to fit residues: 24.5161 Evaluate side-chains 196 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 13 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 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 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 588 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 40 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 65 optimal weight: 20.0000 chunk 14 optimal weight: 0.0980 chunk 32 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3990 r_free = 0.3990 target = 0.157580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.127877 restraints weight = 9015.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.131404 restraints weight = 4415.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.133697 restraints weight = 2607.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.135196 restraints weight = 1765.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.136154 restraints weight = 1339.226| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6206 Z= 0.166 Angle : 0.586 11.718 8530 Z= 0.330 Chirality : 0.044 0.164 957 Planarity : 0.004 0.061 950 Dihedral : 20.511 135.754 1100 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.08 % Favored : 97.76 % Rotamer: Outliers : 3.90 % Allowed : 20.51 % Favored : 75.59 % 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: 0.82 (0.34), residues: 625 helix: 1.34 (0.30), residues: 305 sheet: -0.69 (0.56), residues: 76 loop : 0.10 (0.43), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 337 TYR 0.011 0.001 TYR A 471 PHE 0.027 0.002 PHE A 406 TRP 0.024 0.003 TRP A 512 HIS 0.005 0.001 HIS A 513 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.17 ( 6206) covalent geometry : angle 0.58634 / 0.33 ( 8530) hydrogen bonds : bond 0.04311 / 2.63 ( 306) hydrogen bonds : angle 4.60166 / 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 200 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 177 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.8230 (tttp) cc_final: 0.7972 (tttp) REVERT: A 48 LYS cc_start: 0.8316 (tttt) cc_final: 0.8039 (tptt) REVERT: A 78 TYR cc_start: 0.7936 (p90) cc_final: 0.7234 (p90) REVERT: A 84 GLN cc_start: 0.7589 (mm-40) cc_final: 0.7349 (mm-40) REVERT: A 117 LYS cc_start: 0.7216 (mmtm) cc_final: 0.6996 (mmtm) REVERT: A 170 ASN cc_start: 0.6703 (t0) cc_final: 0.6178 (t0) REVERT: A 200 ASN cc_start: 0.7879 (t0) cc_final: 0.7642 (t0) REVERT: A 210 PHE cc_start: 0.6868 (m-80) cc_final: 0.6627 (m-80) REVERT: A 221 LYS cc_start: 0.7585 (mmmm) cc_final: 0.7349 (mmmm) REVERT: A 251 ASP cc_start: 0.7669 (t0) cc_final: 0.7329 (t70) REVERT: A 253 GLU cc_start: 0.7505 (mt-10) cc_final: 0.7272 (mt-10) REVERT: A 271 ILE cc_start: 0.7030 (OUTLIER) cc_final: 0.6761 (tp) REVERT: A 284 LYS cc_start: 0.7818 (mmmm) cc_final: 0.7464 (mmmm) REVERT: A 335 SER cc_start: 0.8042 (t) cc_final: 0.7777 (p) REVERT: A 366 THR cc_start: 0.8523 (OUTLIER) cc_final: 0.8095 (t) REVERT: A 369 ASN cc_start: 0.7521 (m110) cc_final: 0.7072 (m110) REVERT: A 372 LYS cc_start: 0.7741 (mttm) cc_final: 0.7373 (mttm) REVERT: A 481 TYR cc_start: 0.8255 (t80) cc_final: 0.7963 (t80) REVERT: A 523 GLN cc_start: 0.7612 (tm-30) cc_final: 0.7300 (tm-30) outliers start: 23 outliers final: 19 residues processed: 183 average time/residue: 0.1004 time to fit residues: 22.9848 Evaluate side-chains 196 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 175 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 47 LYS 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 22 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 62 optimal weight: 30.0000 chunk 51 optimal weight: 1.9990 chunk 57 optimal weight: 0.0870 chunk 38 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 3 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- 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 = 0.3987 r_free = 0.3987 target = 0.157355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.127941 restraints weight = 9023.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.131370 restraints weight = 4455.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.133628 restraints weight = 2647.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.135061 restraints weight = 1801.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.135956 restraints weight = 1380.503| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6206 Z= 0.172 Angle : 0.591 12.759 8530 Z= 0.332 Chirality : 0.044 0.156 957 Planarity : 0.004 0.061 950 Dihedral : 20.420 135.644 1100 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.56 % Favored : 97.28 % Rotamer: Outliers : 4.24 % Allowed : 20.51 % Favored : 75.25 % 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: 0.81 (0.34), residues: 625 helix: 1.36 (0.30), residues: 305 sheet: -0.66 (0.56), residues: 76 loop : 0.04 (0.43), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 337 TYR 0.009 0.001 TYR A 42 PHE 0.026 0.002 PHE A 406 TRP 0.009 0.002 TRP A 512 HIS 0.004 0.001 HIS A 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 ( 6206) covalent geometry : angle 0.59132 / 0.33 ( 8530) hydrogen bonds : bond 0.04358 / 2.67 ( 306) hydrogen bonds : angle 4.57832 / 3.16 ( 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 199 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 174 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.8205 (tttp) cc_final: 0.7960 (tttp) REVERT: A 48 LYS cc_start: 0.8313 (tttt) cc_final: 0.8042 (tptt) REVERT: A 78 TYR cc_start: 0.7932 (p90) cc_final: 0.7223 (p90) REVERT: A 93 GLU cc_start: 0.6910 (mm-30) cc_final: 0.6491 (mm-30) REVERT: A 117 LYS cc_start: 0.7207 (mmtm) cc_final: 0.7003 (mmtm) REVERT: A 170 ASN cc_start: 0.6695 (t0) cc_final: 0.6174 (t0) REVERT: A 200 ASN cc_start: 0.7868 (t0) cc_final: 0.7625 (t0) REVERT: A 210 PHE cc_start: 0.6872 (m-80) cc_final: 0.6623 (m-80) REVERT: A 251 ASP cc_start: 0.7647 (t0) cc_final: 0.7169 (t70) REVERT: A 253 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7230 (mt-10) REVERT: A 271 ILE cc_start: 0.7055 (OUTLIER) cc_final: 0.6798 (tp) REVERT: A 284 LYS cc_start: 0.7809 (mmmm) cc_final: 0.7458 (mmmm) REVERT: A 335 SER cc_start: 0.7998 (t) cc_final: 0.7746 (p) REVERT: A 366 THR cc_start: 0.8557 (OUTLIER) cc_final: 0.8244 (t) REVERT: A 369 ASN cc_start: 0.7504 (m110) cc_final: 0.7088 (m110) REVERT: A 372 LYS cc_start: 0.7732 (mttm) cc_final: 0.7372 (mttm) REVERT: A 481 TYR cc_start: 0.8222 (t80) cc_final: 0.7960 (t80) REVERT: A 523 GLN cc_start: 0.7592 (tm-30) cc_final: 0.7286 (tm-30) outliers start: 25 outliers final: 16 residues processed: 181 average time/residue: 0.1015 time to fit residues: 22.9494 Evaluate side-chains 192 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 174 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE 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 353 LEU Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 387 GLN Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 580 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 63 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 62 optimal weight: 30.0000 chunk 17 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 172 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 = 0.3967 r_free = 0.3967 target = 0.155666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.126118 restraints weight = 8996.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.129644 restraints weight = 4424.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.131959 restraints weight = 2609.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.133413 restraints weight = 1773.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.134388 restraints weight = 1352.427| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 6206 Z= 0.262 Angle : 0.644 12.529 8530 Z= 0.358 Chirality : 0.047 0.170 957 Planarity : 0.004 0.063 950 Dihedral : 20.440 135.144 1100 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.72 % Favored : 97.12 % Rotamer: Outliers : 3.39 % Allowed : 22.03 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.34), residues: 625 helix: 0.99 (0.30), residues: 312 sheet: -0.62 (0.56), residues: 76 loop : -0.21 (0.44), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 337 TYR 0.015 0.002 TYR A 471 PHE 0.028 0.002 PHE A 406 TRP 0.012 0.003 TRP A 512 HIS 0.006 0.001 HIS A 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00579 / 0.26 ( 6206) covalent geometry : angle 0.64390 / 0.36 ( 8530) hydrogen bonds : bond 0.04959 / 3.01 ( 306) hydrogen bonds : angle 4.75265 / 3.28 ( 836) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1198.89 seconds wall clock time: 21 minutes 31.65 seconds (1291.65 seconds total)