Starting phenix.real_space_refine on Tue Feb 3 18:25:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9quj_53378/02_2026/9quj_53378.cif Found real_map, /net/cci-nas-00/data/ceres_data/9quj_53378/02_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 { model { file = "/net/cci-nas-00/data/ceres_data/9quj_53378/02_2026/9quj_53378.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9quj_53378/02_2026/9quj_53378.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9quj_53378/02_2026/9quj_53378.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9quj_53378/02_2026/9quj_53378.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 40 5.49 5 S 16 5.16 5 C 3729 2.51 5 N 1027 2.21 5 O 1210 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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: 1.41, per 1000 atoms: 0.23 Number of scatterers: 6022 At special positions: 0 Unit cell: (73.14, 117.66, 111.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 16 16.00 P 40 15.00 O 1210 8.00 N 1027 7.00 C 3729 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.45 Conformation dependent library (CDL) restraints added in 316.3 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: 0.83 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: 1.10 Time building geometry restraints manager: 0.59 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=" N GLN A 387 " pdb=" CA GLN A 387 " ideal model delta sigma weight residual 1.456 1.483 -0.027 1.33e-02 5.65e+03 4.14e+00 bond pdb=" N ASP A 1 " pdb=" CA ASP A 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.85e+00 bond pdb=" C1' DT C 11 " pdb=" N1 DT C 11 " ideal model delta sigma weight residual 1.490 1.538 -0.048 3.00e-02 1.11e+03 2.53e+00 bond pdb=" C LYS A 382 " pdb=" N PRO A 383 " ideal model delta sigma weight residual 1.334 1.369 -0.035 2.34e-02 1.83e+03 2.19e+00 bond pdb=" C3' DA B 13 " pdb=" O3' DA B 13 " ideal model delta sigma weight residual 1.422 1.463 -0.041 3.00e-02 1.11e+03 1.85e+00 ... (remaining 6201 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 8066 1.16 - 2.32: 385 2.32 - 3.48: 59 3.48 - 4.64: 15 4.64 - 5.79: 5 Bond angle restraints: 8530 Sorted by residual: angle pdb=" N GLN A 387 " pdb=" CA GLN A 387 " pdb=" C GLN A 387 " ideal model delta sigma weight residual 113.23 109.87 3.36 1.24e+00 6.50e-01 7.36e+00 angle pdb=" CA LYS A 382 " pdb=" C LYS A 382 " pdb=" N PRO A 383 " ideal model delta sigma weight residual 118.44 122.55 -4.11 1.59e+00 3.96e-01 6.68e+00 angle pdb=" C3' DG B 23 " pdb=" C2' DG B 23 " pdb=" C1' DG B 23 " ideal model delta sigma weight residual 101.60 105.47 -3.87 1.50e+00 4.44e-01 6.67e+00 angle pdb=" C HIS A 578 " pdb=" CA HIS A 578 " pdb=" CB HIS A 578 " ideal model delta sigma weight residual 110.42 115.56 -5.14 1.99e+00 2.53e-01 6.67e+00 angle pdb=" C4' DT C 18 " pdb=" O4' DT C 18 " pdb=" C1' DT C 18 " ideal model delta sigma weight residual 109.70 105.85 3.85 1.50e+00 4.44e-01 6.57e+00 ... (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 - 0.030: 553 0.030 - 0.060: 260 0.060 - 0.090: 84 0.090 - 0.120: 46 0.120 - 0.150: 14 Chirality restraints: 957 Sorted by residual: chirality pdb=" CA ILE A 388 " pdb=" N ILE A 388 " pdb=" C ILE A 388 " pdb=" CB ILE A 388 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.60e-01 chirality pdb=" CA ILE A 98 " pdb=" N ILE A 98 " pdb=" C ILE A 98 " pdb=" CB ILE A 98 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.65e-01 chirality pdb=" CG LEU A 186 " pdb=" CB LEU A 186 " pdb=" CD1 LEU A 186 " pdb=" CD2 LEU A 186 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.60e-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: 1.070 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: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.410 Find NCS groups from input model: 0.040 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 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 : 0.005 0.051 6206 Z= 0.231 Angle : 0.588 5.795 8530 Z= 0.347 Chirality : 0.043 0.150 957 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 covalent geometry : bond 0.00504 ( 6206) covalent geometry : angle 0.58787 ( 8530) hydrogen bonds : bond 0.15833 ( 306) hydrogen bonds : angle 6.69703 ( 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 : 0.216 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: 0.1033 time to fit residues: 25.8347 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 : 0.272 ------------------------------------------------------------------------------- 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: 6.9990 chunk 62 optimal weight: 5.9990 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... Flipped N/Q/H residues before XYZ refinement: 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 306 ASN A 386 GLN A 387 GLN A 513 HIS A 623 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.157878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.127505 restraints weight = 9133.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.131108 restraints weight = 4491.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.133454 restraints weight = 2641.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.134911 restraints weight = 1785.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.135880 restraints weight = 1359.136| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.1383 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= 0.190 Angle : 0.576 6.389 8530 Z= 0.323 Chirality : 0.045 0.176 957 Planarity : 0.004 0.048 950 Dihedral : 20.357 137.119 1100 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.56 % Favored : 97.28 % Rotamer: Outliers : 3.05 % Allowed : 13.90 % Favored : 83.05 % 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: 0.49 (0.35), residues: 625 helix: 1.01 (0.30), residues: 311 sheet: -0.73 (0.59), residues: 76 loop : -0.05 (0.45), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 214 TYR 0.010 0.001 TYR A 110 PHE 0.016 0.002 PHE A 406 TRP 0.012 0.002 TRP A 624 HIS 0.002 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 6206) covalent geometry : angle 0.57639 ( 8530) hydrogen bonds : bond 0.05042 ( 306) hydrogen bonds : angle 5.01497 ( 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 201 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 183 time to evaluate : 0.221 Fit side-chains REVERT: A 6 LYS cc_start: 0.7448 (tttm) cc_final: 0.6934 (tttp) REVERT: A 13 ILE cc_start: 0.8208 (tt) cc_final: 0.7837 (pt) REVERT: A 21 LYS cc_start: 0.8126 (tttp) cc_final: 0.7846 (tptt) REVERT: A 48 LYS cc_start: 0.8317 (tttt) cc_final: 0.8058 (tptt) REVERT: A 78 TYR cc_start: 0.8017 (p90) cc_final: 0.7478 (p90) REVERT: A 93 GLU cc_start: 0.6840 (mm-30) cc_final: 0.6625 (mm-30) REVERT: A 103 GLU cc_start: 0.7753 (tt0) cc_final: 0.7441 (tt0) REVERT: A 117 LYS cc_start: 0.7365 (mmtm) cc_final: 0.7018 (mmtm) REVERT: A 170 ASN cc_start: 0.6777 (t0) cc_final: 0.6453 (t0) REVERT: A 200 ASN cc_start: 0.7856 (t0) cc_final: 0.7647 (t0) REVERT: A 210 PHE cc_start: 0.6882 (m-80) cc_final: 0.6602 (m-80) REVERT: A 251 ASP cc_start: 0.7736 (t70) cc_final: 0.7412 (t70) REVERT: A 252 MET cc_start: 0.7546 (mtp) cc_final: 0.7337 (mtp) REVERT: A 284 LYS cc_start: 0.7843 (mmmm) cc_final: 0.7001 (mmmm) REVERT: A 287 LYS cc_start: 0.8539 (mmmt) cc_final: 0.8128 (mmmt) REVERT: A 335 SER cc_start: 0.8133 (t) cc_final: 0.7876 (p) REVERT: A 352 LYS cc_start: 0.7856 (mtpp) cc_final: 0.7636 (mtpp) REVERT: A 369 ASN cc_start: 0.7733 (m-40) cc_final: 0.7160 (m-40) REVERT: A 372 LYS cc_start: 0.7750 (mttm) cc_final: 0.7377 (mttm) REVERT: A 378 PHE cc_start: 0.7710 (m-80) cc_final: 0.7364 (m-80) REVERT: A 481 TYR cc_start: 0.8306 (t80) cc_final: 0.8021 (t80) REVERT: A 523 GLN cc_start: 0.7704 (tm-30) cc_final: 0.7317 (tm-30) outliers start: 18 outliers final: 11 residues processed: 188 average time/residue: 0.0961 time to fit residues: 22.2540 Evaluate side-chains 188 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 177 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASN Chi-restraints excluded: chain A residue 47 LYS 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 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: 0.6980 chunk 59 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN ** A 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.157430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.127723 restraints weight = 9014.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.131210 restraints weight = 4400.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.133447 restraints weight = 2573.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.134891 restraints weight = 1740.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.135783 restraints weight = 1323.944| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 moved from start: 0.1733 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= 0.181 Angle : 0.552 6.961 8530 Z= 0.308 Chirality : 0.044 0.156 957 Planarity : 0.003 0.052 950 Dihedral : 20.462 137.086 1100 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.56 % Favored : 97.28 % Rotamer: Outliers : 3.56 % Allowed : 15.76 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.35), residues: 625 helix: 1.12 (0.30), residues: 311 sheet: -0.83 (0.58), residues: 76 loop : -0.04 (0.44), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 341 TYR 0.010 0.001 TYR A 73 PHE 0.016 0.002 PHE A 539 TRP 0.007 0.002 TRP A 199 HIS 0.004 0.001 HIS A 236 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 6206) covalent geometry : angle 0.55234 ( 8530) hydrogen bonds : bond 0.04677 ( 306) hydrogen bonds : angle 4.75133 ( 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 199 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 178 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.8159 (tttp) cc_final: 0.7948 (tttp) REVERT: A 48 LYS cc_start: 0.8331 (tttt) cc_final: 0.8052 (tptt) REVERT: A 78 TYR cc_start: 0.7964 (p90) cc_final: 0.7316 (p90) REVERT: A 117 LYS cc_start: 0.7345 (mmtm) cc_final: 0.7016 (mmtm) REVERT: A 170 ASN cc_start: 0.6755 (t0) cc_final: 0.6230 (t0) REVERT: A 200 ASN cc_start: 0.7875 (t0) cc_final: 0.7634 (t0) REVERT: A 210 PHE cc_start: 0.6923 (m-80) cc_final: 0.6536 (m-80) REVERT: A 251 ASP cc_start: 0.7711 (t70) cc_final: 0.7415 (t70) REVERT: A 284 LYS cc_start: 0.7854 (mmmm) cc_final: 0.7483 (mmmm) REVERT: A 321 ASP cc_start: 0.7111 (t0) cc_final: 0.6675 (t0) REVERT: A 335 SER cc_start: 0.8148 (t) cc_final: 0.7862 (p) REVERT: A 352 LYS cc_start: 0.7875 (mtpp) cc_final: 0.7640 (mtpp) REVERT: A 369 ASN cc_start: 0.7553 (m-40) cc_final: 0.7088 (m-40) REVERT: A 372 LYS cc_start: 0.7762 (mttm) cc_final: 0.7396 (mttm) REVERT: A 378 PHE cc_start: 0.7754 (m-80) cc_final: 0.7377 (m-80) REVERT: A 387 GLN cc_start: 0.7149 (OUTLIER) cc_final: 0.6932 (tp-100) REVERT: A 395 ARG cc_start: 0.7339 (mmm160) cc_final: 0.7090 (mmm160) REVERT: A 481 TYR cc_start: 0.8336 (t80) cc_final: 0.8034 (t80) REVERT: A 490 MET cc_start: 0.6318 (OUTLIER) cc_final: 0.6021 (tmm) REVERT: A 523 GLN cc_start: 0.7654 (tm-30) cc_final: 0.7315 (tm-30) outliers start: 21 outliers final: 16 residues processed: 185 average time/residue: 0.0997 time to fit residues: 22.6662 Evaluate side-chains 194 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 176 time to evaluate : 0.173 ------------------------------------------------------------------------------- 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 246 ILE 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 374 PHE Chi-restraints excluded: chain A residue 387 GLN 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 490 MET 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 62 optimal weight: 7.9990 chunk 43 optimal weight: 0.0270 chunk 34 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 61 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 47 optimal weight: 0.4980 chunk 35 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN ** A 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 369 ASN A 466 ASN A 513 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.158485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.128919 restraints weight = 9026.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.132406 restraints weight = 4390.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.134663 restraints weight = 2571.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.136101 restraints weight = 1738.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.137045 restraints weight = 1320.242| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6206 Z= 0.147 Angle : 0.532 8.275 8530 Z= 0.298 Chirality : 0.042 0.154 957 Planarity : 0.003 0.055 950 Dihedral : 20.462 137.167 1100 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.92 % Favored : 97.92 % Rotamer: Outliers : 4.24 % Allowed : 16.95 % Favored : 78.81 % 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: 0.68 (0.35), residues: 625 helix: 1.24 (0.30), residues: 312 sheet: -0.74 (0.58), residues: 76 loop : -0.05 (0.44), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 341 TYR 0.007 0.001 TYR A 346 PHE 0.017 0.001 PHE A 539 TRP 0.006 0.001 TRP A 199 HIS 0.014 0.002 HIS A 513 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 6206) covalent geometry : angle 0.53218 ( 8530) hydrogen bonds : bond 0.04244 ( 306) hydrogen bonds : angle 4.58621 ( 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 200 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 175 time to evaluate : 0.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.8158 (tttp) cc_final: 0.7828 (tttp) REVERT: A 48 LYS cc_start: 0.8309 (tttt) cc_final: 0.8033 (tptt) REVERT: A 78 TYR cc_start: 0.7970 (p90) cc_final: 0.7259 (p90) REVERT: A 93 GLU cc_start: 0.6883 (mm-30) cc_final: 0.6530 (mm-30) REVERT: A 117 LYS cc_start: 0.7277 (mmtm) cc_final: 0.6968 (mmtm) REVERT: A 170 ASN cc_start: 0.6685 (t0) cc_final: 0.6170 (t0) REVERT: A 200 ASN cc_start: 0.7835 (t0) cc_final: 0.7601 (t0) REVERT: A 210 PHE cc_start: 0.6943 (m-80) cc_final: 0.6567 (m-80) REVERT: A 214 ARG cc_start: 0.7793 (mtp85) cc_final: 0.7493 (mtp85) REVERT: A 251 ASP cc_start: 0.7676 (t70) cc_final: 0.7202 (t70) REVERT: A 252 MET cc_start: 0.7290 (mtp) cc_final: 0.7084 (mtp) REVERT: A 321 ASP cc_start: 0.7078 (t0) cc_final: 0.6494 (t0) REVERT: A 335 SER cc_start: 0.8076 (t) cc_final: 0.7769 (p) REVERT: A 369 ASN cc_start: 0.7446 (m110) cc_final: 0.7045 (m-40) REVERT: A 372 LYS cc_start: 0.7753 (mttm) cc_final: 0.7378 (mttm) REVERT: A 378 PHE cc_start: 0.7751 (m-80) cc_final: 0.7334 (m-80) REVERT: A 481 TYR cc_start: 0.8262 (t80) cc_final: 0.7945 (t80) REVERT: A 490 MET cc_start: 0.6272 (OUTLIER) cc_final: 0.5930 (tmm) REVERT: A 523 GLN cc_start: 0.7634 (tm-30) cc_final: 0.7323 (tm-30) REVERT: A 575 LEU cc_start: 0.8643 (tp) cc_final: 0.8421 (tp) outliers start: 25 outliers final: 17 residues processed: 182 average time/residue: 0.0954 time to fit residues: 21.3920 Evaluate side-chains 190 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 172 time to evaluate : 0.132 ------------------------------------------------------------------------------- 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 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 374 PHE Chi-restraints excluded: chain A residue 387 GLN Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 490 MET 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: 3.9990 chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 43 optimal weight: 0.0970 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN ** A 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.158143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.128480 restraints weight = 9104.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.131989 restraints weight = 4429.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.134278 restraints weight = 2588.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.135752 restraints weight = 1753.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.136572 restraints weight = 1327.509| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.2116 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= 0.162 Angle : 0.533 8.579 8530 Z= 0.296 Chirality : 0.042 0.157 957 Planarity : 0.004 0.057 950 Dihedral : 20.451 137.115 1100 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.08 % Favored : 97.76 % Rotamer: Outliers : 4.75 % Allowed : 18.14 % Favored : 77.12 % 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: 0.70 (0.35), residues: 625 helix: 1.23 (0.30), residues: 313 sheet: -0.68 (0.57), residues: 76 loop : -0.01 (0.44), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 341 TYR 0.009 0.001 TYR A 42 PHE 0.017 0.002 PHE A 539 TRP 0.006 0.002 TRP A 199 HIS 0.003 0.001 HIS A 236 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 6206) covalent geometry : angle 0.53267 ( 8530) hydrogen bonds : bond 0.04226 ( 306) hydrogen bonds : angle 4.52475 ( 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 204 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 176 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.8206 (tttp) cc_final: 0.7975 (tttp) REVERT: A 48 LYS cc_start: 0.8287 (tttt) cc_final: 0.7999 (tptt) REVERT: A 78 TYR cc_start: 0.7951 (p90) cc_final: 0.7238 (p90) REVERT: A 93 GLU cc_start: 0.6791 (mm-30) cc_final: 0.6572 (mm-30) REVERT: A 170 ASN cc_start: 0.6698 (t0) cc_final: 0.6173 (t0) REVERT: A 200 ASN cc_start: 0.7862 (t0) cc_final: 0.7629 (t0) REVERT: A 210 PHE cc_start: 0.6955 (m-80) cc_final: 0.6515 (m-80) REVERT: A 251 ASP cc_start: 0.7661 (t70) cc_final: 0.7190 (t70) REVERT: A 253 GLU cc_start: 0.7442 (mt-10) cc_final: 0.7162 (mt-10) REVERT: A 271 ILE cc_start: 0.7003 (OUTLIER) cc_final: 0.6786 (tp) REVERT: A 284 LYS cc_start: 0.7799 (mmmm) cc_final: 0.7440 (mmmm) REVERT: A 335 SER cc_start: 0.8093 (t) cc_final: 0.7767 (p) REVERT: A 352 LYS cc_start: 0.7788 (mtpp) cc_final: 0.7584 (mtpp) REVERT: A 369 ASN cc_start: 0.7442 (m110) cc_final: 0.7079 (m-40) REVERT: A 372 LYS cc_start: 0.7757 (mttm) cc_final: 0.7377 (mttm) REVERT: A 481 TYR cc_start: 0.8233 (t80) cc_final: 0.7948 (t80) REVERT: A 523 GLN cc_start: 0.7626 (tm-30) cc_final: 0.7308 (tm-30) outliers start: 28 outliers final: 20 residues processed: 183 average time/residue: 0.0988 time to fit residues: 22.2994 Evaluate side-chains 194 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 173 time to evaluate : 0.212 ------------------------------------------------------------------------------- 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 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 353 LEU Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 513 HIS Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 602 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 41 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN A 391 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 = 0.3980 r_free = 0.3980 target = 0.156865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.127485 restraints weight = 8916.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.131000 restraints weight = 4393.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.133335 restraints weight = 2574.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.134706 restraints weight = 1734.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.135598 restraints weight = 1326.382| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.2227 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= 0.188 Angle : 0.553 10.251 8530 Z= 0.306 Chirality : 0.043 0.166 957 Planarity : 0.003 0.058 950 Dihedral : 20.459 136.768 1100 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.72 % Favored : 97.12 % Rotamer: Outliers : 4.41 % Allowed : 18.98 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.35), residues: 625 helix: 1.31 (0.30), residues: 305 sheet: -0.68 (0.57), residues: 76 loop : 0.01 (0.43), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 337 TYR 0.010 0.001 TYR A 42 PHE 0.026 0.002 PHE A 406 TRP 0.007 0.002 TRP A 199 HIS 0.011 0.002 HIS A 513 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 6206) covalent geometry : angle 0.55268 ( 8530) hydrogen bonds : bond 0.04319 ( 306) hydrogen bonds : angle 4.58045 ( 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 201 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 175 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.7408 (tttm) cc_final: 0.6891 (tttp) REVERT: A 21 LYS cc_start: 0.8212 (tttp) cc_final: 0.7984 (tttp) REVERT: A 78 TYR cc_start: 0.7933 (p90) cc_final: 0.7288 (p90) REVERT: A 93 GLU cc_start: 0.6793 (mm-30) cc_final: 0.6556 (mm-30) REVERT: A 117 LYS cc_start: 0.7232 (mmtm) cc_final: 0.6966 (mmtm) REVERT: A 170 ASN cc_start: 0.6713 (t0) cc_final: 0.6184 (t0) REVERT: A 200 ASN cc_start: 0.7872 (t0) cc_final: 0.7640 (t0) REVERT: A 210 PHE cc_start: 0.6952 (m-80) cc_final: 0.6560 (m-80) REVERT: A 251 ASP cc_start: 0.7632 (t70) cc_final: 0.7310 (t70) REVERT: A 253 GLU cc_start: 0.7462 (mt-10) cc_final: 0.7182 (mt-10) REVERT: A 271 ILE cc_start: 0.7091 (OUTLIER) cc_final: 0.6821 (tp) REVERT: A 284 LYS cc_start: 0.7803 (mmmm) cc_final: 0.7446 (mmmm) REVERT: A 296 GLN cc_start: 0.6338 (mt0) cc_final: 0.6128 (mt0) REVERT: A 335 SER cc_start: 0.8104 (t) cc_final: 0.7873 (p) REVERT: A 352 LYS cc_start: 0.7763 (mtpp) cc_final: 0.7540 (mtpp) REVERT: A 369 ASN cc_start: 0.7424 (m110) cc_final: 0.7055 (m-40) REVERT: A 372 LYS cc_start: 0.7746 (mttm) cc_final: 0.7364 (mttm) REVERT: A 481 TYR cc_start: 0.8234 (t80) cc_final: 0.7972 (t80) REVERT: A 523 GLN cc_start: 0.7631 (tm-30) cc_final: 0.7305 (tm-30) outliers start: 26 outliers final: 20 residues processed: 182 average time/residue: 0.1007 time to fit residues: 22.7282 Evaluate side-chains 194 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 173 time to evaluate : 0.216 ------------------------------------------------------------------------------- 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 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 353 LEU 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 477 ASN Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 513 HIS 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: 0.9990 chunk 18 optimal weight: 1.9990 chunk 59 optimal weight: 0.4980 chunk 39 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 3 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3986 r_free = 0.3986 target = 0.157435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.127859 restraints weight = 9011.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.131393 restraints weight = 4433.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.133719 restraints weight = 2603.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.135086 restraints weight = 1767.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.136061 restraints weight = 1355.660| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6206 Z= 0.160 Angle : 0.552 11.401 8530 Z= 0.301 Chirality : 0.043 0.163 957 Planarity : 0.003 0.058 950 Dihedral : 20.430 136.600 1100 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.24 % Favored : 97.60 % Rotamer: Outliers : 4.41 % Allowed : 18.98 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.35), residues: 625 helix: 1.35 (0.30), residues: 305 sheet: -0.69 (0.57), residues: 76 loop : 0.02 (0.43), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 337 TYR 0.008 0.001 TYR A 471 PHE 0.023 0.002 PHE A 406 TRP 0.006 0.002 TRP A 199 HIS 0.004 0.001 HIS A 513 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 6206) covalent geometry : angle 0.55186 ( 8530) hydrogen bonds : bond 0.04077 ( 306) hydrogen bonds : angle 4.52343 ( 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 203 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 177 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.8178 (tttp) cc_final: 0.7940 (tttp) REVERT: A 78 TYR cc_start: 0.7886 (p90) cc_final: 0.7187 (p90) REVERT: A 93 GLU cc_start: 0.6768 (mm-30) cc_final: 0.6535 (mm-30) REVERT: A 117 LYS cc_start: 0.7184 (mmtm) cc_final: 0.6924 (mmtm) REVERT: A 170 ASN cc_start: 0.6707 (t0) cc_final: 0.6174 (t0) REVERT: A 200 ASN cc_start: 0.7862 (t0) cc_final: 0.7630 (t0) REVERT: A 210 PHE cc_start: 0.6948 (m-80) cc_final: 0.6493 (m-80) REVERT: A 251 ASP cc_start: 0.7650 (t70) cc_final: 0.7145 (t70) REVERT: A 253 GLU cc_start: 0.7415 (mt-10) cc_final: 0.7109 (mt-10) REVERT: A 271 ILE cc_start: 0.7072 (OUTLIER) cc_final: 0.6785 (tp) REVERT: A 284 LYS cc_start: 0.7805 (mmmm) cc_final: 0.7457 (mmmm) REVERT: A 296 GLN cc_start: 0.6373 (mt0) cc_final: 0.6156 (mt0) REVERT: A 335 SER cc_start: 0.8093 (t) cc_final: 0.7806 (p) REVERT: A 352 LYS cc_start: 0.7687 (mtpp) cc_final: 0.7451 (mtpp) REVERT: A 369 ASN cc_start: 0.7437 (m110) cc_final: 0.7032 (m-40) REVERT: A 372 LYS cc_start: 0.7744 (mttm) cc_final: 0.7359 (mttm) REVERT: A 429 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7442 (mt) REVERT: A 481 TYR cc_start: 0.8206 (t80) cc_final: 0.7940 (t80) REVERT: A 523 GLN cc_start: 0.7615 (tm-30) cc_final: 0.7304 (tm-30) outliers start: 26 outliers final: 22 residues processed: 184 average time/residue: 0.1098 time to fit residues: 24.9749 Evaluate side-chains 198 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 174 time to evaluate : 0.220 ------------------------------------------------------------------------------- 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 353 LEU 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 429 LEU 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 602 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 47 optimal weight: 2.9990 chunk 32 optimal weight: 0.0980 chunk 34 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.156112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.126463 restraints weight = 9051.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.129924 restraints weight = 4524.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.132229 restraints weight = 2683.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.133574 restraints weight = 1833.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.134535 restraints weight = 1413.479| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 6206 Z= 0.203 Angle : 0.578 12.504 8530 Z= 0.314 Chirality : 0.044 0.162 957 Planarity : 0.004 0.059 950 Dihedral : 20.442 136.263 1100 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.88 % Favored : 96.96 % Rotamer: Outliers : 4.07 % Allowed : 19.66 % 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: 0.69 (0.34), residues: 625 helix: 1.29 (0.30), residues: 304 sheet: -0.71 (0.56), residues: 76 loop : -0.06 (0.43), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 337 TYR 0.010 0.001 TYR A 42 PHE 0.023 0.002 PHE A 406 TRP 0.007 0.002 TRP A 199 HIS 0.005 0.001 HIS A 236 Details of bonding type rmsd covalent geometry : bond 0.00456 ( 6206) covalent geometry : angle 0.57804 ( 8530) hydrogen bonds : bond 0.04359 ( 306) hydrogen bonds : angle 4.58183 ( 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 202 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 178 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.7390 (tttm) cc_final: 0.6884 (tttp) REVERT: A 13 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.7898 (pt) REVERT: A 21 LYS cc_start: 0.8159 (tttp) cc_final: 0.7933 (tttp) REVERT: A 78 TYR cc_start: 0.7895 (p90) cc_final: 0.7253 (p90) REVERT: A 117 LYS cc_start: 0.7230 (mmtm) cc_final: 0.6942 (mmtm) REVERT: A 126 LYS cc_start: 0.7712 (mmmt) cc_final: 0.7472 (mmmt) REVERT: A 170 ASN cc_start: 0.6738 (t0) cc_final: 0.6190 (t0) REVERT: A 200 ASN cc_start: 0.7868 (t0) cc_final: 0.7634 (t0) REVERT: A 210 PHE cc_start: 0.6955 (m-80) cc_final: 0.6538 (m-80) REVERT: A 251 ASP cc_start: 0.7630 (t70) cc_final: 0.7335 (t70) REVERT: A 253 GLU cc_start: 0.7411 (mt-10) cc_final: 0.7112 (mt-10) REVERT: A 271 ILE cc_start: 0.7085 (OUTLIER) cc_final: 0.6813 (tp) REVERT: A 284 LYS cc_start: 0.7812 (mmmm) cc_final: 0.7464 (mmmm) REVERT: A 335 SER cc_start: 0.8085 (t) cc_final: 0.7844 (p) REVERT: A 369 ASN cc_start: 0.7413 (m110) cc_final: 0.7026 (m-40) REVERT: A 372 LYS cc_start: 0.7743 (mttm) cc_final: 0.7354 (mttm) REVERT: A 429 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7475 (mt) REVERT: A 481 TYR cc_start: 0.8219 (t80) cc_final: 0.7994 (t80) REVERT: A 523 GLN cc_start: 0.7618 (tm-30) cc_final: 0.7284 (tm-30) REVERT: A 626 SER cc_start: 0.7995 (t) cc_final: 0.7638 (p) outliers start: 24 outliers final: 17 residues processed: 187 average time/residue: 0.0843 time to fit residues: 19.7312 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 : 0.133 ------------------------------------------------------------------------------- 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 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 374 PHE Chi-restraints excluded: chain A residue 387 GLN Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 429 LEU 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 566 LEU Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 580 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 40 optimal weight: 0.4980 chunk 37 optimal weight: 0.0870 chunk 27 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 14 optimal weight: 0.4980 chunk 32 optimal weight: 0.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN A 513 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.157742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.128125 restraints weight = 9060.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.131644 restraints weight = 4489.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.133967 restraints weight = 2639.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.135291 restraints weight = 1788.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.136295 restraints weight = 1378.270| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6206 Z= 0.161 Angle : 0.578 13.323 8530 Z= 0.312 Chirality : 0.043 0.156 957 Planarity : 0.003 0.058 950 Dihedral : 20.326 136.016 1100 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.56 % Favored : 97.28 % Rotamer: Outliers : 3.56 % Allowed : 20.51 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.34), residues: 625 helix: 1.32 (0.30), residues: 305 sheet: -0.70 (0.56), residues: 76 loop : -0.05 (0.43), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 337 TYR 0.019 0.001 TYR A 471 PHE 0.022 0.002 PHE A 406 TRP 0.007 0.002 TRP A 199 HIS 0.005 0.001 HIS A 439 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 6206) covalent geometry : angle 0.57778 ( 8530) hydrogen bonds : bond 0.04020 ( 306) hydrogen bonds : angle 4.50835 ( 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 197 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 176 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.8154 (tttp) cc_final: 0.7914 (tttp) REVERT: A 48 LYS cc_start: 0.8280 (tttt) cc_final: 0.7961 (tptt) REVERT: A 78 TYR cc_start: 0.7877 (p90) cc_final: 0.7170 (p90) REVERT: A 93 GLU cc_start: 0.6931 (mm-30) cc_final: 0.6580 (mm-30) REVERT: A 117 LYS cc_start: 0.7182 (mmtm) cc_final: 0.6885 (mmtm) REVERT: A 170 ASN cc_start: 0.6724 (t0) cc_final: 0.6174 (t0) REVERT: A 200 ASN cc_start: 0.7858 (t0) cc_final: 0.7630 (t0) REVERT: A 210 PHE cc_start: 0.6959 (m-80) cc_final: 0.6484 (m-80) REVERT: A 214 ARG cc_start: 0.7866 (mtp85) cc_final: 0.7628 (mtm180) REVERT: A 221 LYS cc_start: 0.7650 (mmmm) cc_final: 0.7295 (mmtm) REVERT: A 251 ASP cc_start: 0.7640 (t70) cc_final: 0.7156 (t70) REVERT: A 253 GLU cc_start: 0.7402 (mt-10) cc_final: 0.7118 (mt-10) REVERT: A 271 ILE cc_start: 0.7015 (OUTLIER) cc_final: 0.6742 (tp) REVERT: A 284 LYS cc_start: 0.7820 (mmmm) cc_final: 0.7473 (mmmm) REVERT: A 335 SER cc_start: 0.8068 (t) cc_final: 0.7819 (p) REVERT: A 369 ASN cc_start: 0.7389 (m110) cc_final: 0.6950 (m110) REVERT: A 372 LYS cc_start: 0.7695 (mttm) cc_final: 0.7283 (mttm) REVERT: A 429 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7423 (mt) REVERT: A 481 TYR cc_start: 0.8225 (t80) cc_final: 0.7974 (t80) REVERT: A 523 GLN cc_start: 0.7623 (tm-30) cc_final: 0.7303 (tm-30) REVERT: A 626 SER cc_start: 0.7980 (t) cc_final: 0.7628 (p) outliers start: 21 outliers final: 17 residues processed: 183 average time/residue: 0.1035 time to fit residues: 23.5885 Evaluate side-chains 194 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 175 time to evaluate : 0.220 ------------------------------------------------------------------------------- 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 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 374 PHE Chi-restraints excluded: chain A residue 387 GLN Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 568 ASP 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 22 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 chunk 38 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3980 r_free = 0.3980 target = 0.156604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.127028 restraints weight = 9044.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.130562 restraints weight = 4468.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.132744 restraints weight = 2650.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.134233 restraints weight = 1811.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.135228 restraints weight = 1381.171| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6206 Z= 0.179 Angle : 0.591 14.017 8530 Z= 0.319 Chirality : 0.044 0.172 957 Planarity : 0.003 0.059 950 Dihedral : 20.093 135.823 1100 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.04 % Favored : 96.80 % Rotamer: Outliers : 3.39 % Allowed : 21.02 % 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: 0.66 (0.35), residues: 625 helix: 1.26 (0.30), residues: 305 sheet: -0.70 (0.56), residues: 76 loop : -0.09 (0.43), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 337 TYR 0.016 0.001 TYR A 471 PHE 0.024 0.002 PHE A 406 TRP 0.008 0.002 TRP A 512 HIS 0.005 0.001 HIS A 513 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 6206) covalent geometry : angle 0.59051 ( 8530) hydrogen bonds : bond 0.04149 ( 306) hydrogen bonds : angle 4.52338 ( 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 192 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 172 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.7372 (tttm) cc_final: 0.6885 (tttp) REVERT: A 21 LYS cc_start: 0.8193 (tttp) cc_final: 0.7982 (tttp) REVERT: A 27 LYS cc_start: 0.7399 (mtmt) cc_final: 0.6977 (mmmt) REVERT: A 48 LYS cc_start: 0.8264 (tttt) cc_final: 0.7967 (tptt) REVERT: A 78 TYR cc_start: 0.7872 (p90) cc_final: 0.7162 (p90) REVERT: A 93 GLU cc_start: 0.6876 (mm-30) cc_final: 0.6513 (mm-30) REVERT: A 117 LYS cc_start: 0.7163 (mmtm) cc_final: 0.6896 (mmtm) REVERT: A 126 LYS cc_start: 0.7679 (mmmt) cc_final: 0.7458 (mmmt) REVERT: A 170 ASN cc_start: 0.6721 (t0) cc_final: 0.6172 (t0) REVERT: A 200 ASN cc_start: 0.7855 (t0) cc_final: 0.7630 (t0) REVERT: A 210 PHE cc_start: 0.6965 (m-80) cc_final: 0.6509 (m-80) REVERT: A 221 LYS cc_start: 0.7720 (mmmm) cc_final: 0.7350 (mmtm) REVERT: A 251 ASP cc_start: 0.7634 (t70) cc_final: 0.7169 (t70) REVERT: A 253 GLU cc_start: 0.7425 (mt-10) cc_final: 0.7144 (mt-10) REVERT: A 271 ILE cc_start: 0.7046 (OUTLIER) cc_final: 0.6789 (tp) REVERT: A 284 LYS cc_start: 0.7813 (mmmm) cc_final: 0.7474 (mmmm) REVERT: A 335 SER cc_start: 0.8074 (t) cc_final: 0.7825 (p) REVERT: A 369 ASN cc_start: 0.7315 (m110) cc_final: 0.6840 (m110) REVERT: A 372 LYS cc_start: 0.7683 (mttm) cc_final: 0.7273 (mttm) REVERT: A 429 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7493 (mt) REVERT: A 481 TYR cc_start: 0.8204 (t80) cc_final: 0.7996 (t80) REVERT: A 626 SER cc_start: 0.7975 (t) cc_final: 0.7619 (p) outliers start: 20 outliers final: 16 residues processed: 178 average time/residue: 0.0907 time to fit residues: 20.1456 Evaluate side-chains 189 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 171 time to evaluate : 0.226 ------------------------------------------------------------------------------- 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 353 LEU Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 568 ASP 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: 3.9990 chunk 31 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 17 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.154829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.125472 restraints weight = 9003.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.128997 restraints weight = 4448.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.131241 restraints weight = 2644.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.132714 restraints weight = 1793.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.133566 restraints weight = 1358.880| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 6206 Z= 0.254 Angle : 0.635 13.553 8530 Z= 0.343 Chirality : 0.046 0.163 957 Planarity : 0.004 0.061 950 Dihedral : 20.178 134.502 1100 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.88 % Favored : 96.96 % Rotamer: Outliers : 3.22 % Allowed : 21.69 % Favored : 75.08 % 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: 0.41 (0.34), residues: 625 helix: 1.04 (0.30), residues: 304 sheet: -0.81 (0.57), residues: 78 loop : -0.19 (0.43), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 337 TYR 0.014 0.002 TYR A 471 PHE 0.026 0.003 PHE A 406 TRP 0.009 0.002 TRP A 199 HIS 0.007 0.002 HIS A 513 Details of bonding type rmsd covalent geometry : bond 0.00575 ( 6206) covalent geometry : angle 0.63529 ( 8530) hydrogen bonds : bond 0.04701 ( 306) hydrogen bonds : angle 4.68371 ( 836) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1104.23 seconds wall clock time: 19 minutes 44.14 seconds (1184.14 seconds total)