Starting phenix.real_space_refine on Wed Jul 1 22:15:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wrj_32728/07_2026/7wrj_32728.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wrj_32728/07_2026/7wrj_32728.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7wrj_32728/07_2026/7wrj_32728.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wrj_32728/07_2026/7wrj_32728.cif" model { file = "/net/cci-nas-00/data/ceres_data/7wrj_32728/07_2026/7wrj_32728.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wrj_32728/07_2026/7wrj_32728.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wrj_32728/07_2026/7wrj_32728.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wrj_32728/07_2026/7wrj_32728.map" } resolution = 4.08 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 14 5.16 5 C 2091 2.51 5 N 557 2.21 5 O 627 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3289 Number of models: 1 Model: "" Number of chains: 4 Chain: "R" Number of atoms: 1504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1504 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 10, 'TRANS': 176} Chain breaks: 1 Chain: "A" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 973 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 7, 'TRANS': 117} Chain: "B" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 784 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 0.93, per 1000 atoms: 0.28 Number of scatterers: 3289 At special positions: 0 Unit cell: (73.83, 75.97, 85.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 14 16.00 O 627 8.00 N 557 7.00 C 2091 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.03 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.03 Simple disulfide: pdb=" SG CYS R 391 " - pdb=" SG CYS R 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 97 " distance=2.02 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 89 " distance=2.04 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG C 1 " - " ASN R 343 " Time building additional restraints: 0.26 Conformation dependent library (CDL) restraints added in 102.4 milliseconds 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 768 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 9 sheets defined 7.7% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'R' and resid 364 through 368 Processing helix chain 'R' and resid 403 through 407 removed outlier: 3.704A pdb=" N VAL R 407 " --> pdb=" O GLY R 404 " (cutoff:3.500A) Processing helix chain 'R' and resid 416 through 422 Processing helix chain 'R' and resid 502 through 506 Processing helix chain 'A' and resid 88 through 92 Processing helix chain 'B' and resid 80 through 84 removed outlier: 3.954A pdb=" N ASP B 83 " --> pdb=" O GLN B 80 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLU B 84 " --> pdb=" O SER B 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 80 through 84' Processing sheet with id=AA1, first strand: chain 'R' and resid 354 through 358 removed outlier: 3.628A pdb=" N VAL R 395 " --> pdb=" O ILE R 358 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL R 512 " --> pdb=" O ASP R 398 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.510A pdb=" N THR A 83 " --> pdb=" O THR A 70 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.589A pdb=" N ALA A 98 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL A 36 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LEU A 52 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N TRP A 38 " --> pdb=" O LEU A 50 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 52 " --> pdb=" O ARG A 60 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG A 60 " --> pdb=" O LEU A 52 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.868A pdb=" N MET A 115 " --> pdb=" O HIS A 99 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 9 through 10 Processing sheet with id=AA7, first strand: chain 'B' and resid 18 through 19 Processing sheet with id=AA8, first strand: chain 'B' and resid 22 through 23 Processing sheet with id=AA9, first strand: chain 'B' and resid 45 through 49 removed outlier: 5.736A pdb=" N LEU B 47 " --> pdb=" O GLN B 38 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N GLN B 38 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU B 90 " --> pdb=" O ASN B 35 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY B 98 " --> pdb=" O ASP B 93 " (cutoff:3.500A) 82 hydrogen bonds defined for protein. 174 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.33 Time building geometry restraints manager: 0.32 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: 997 1.33 - 1.46: 912 1.46 - 1.59: 1448 1.59 - 1.72: 1 1.72 - 1.85: 15 Bond restraints: 3373 Sorted by residual: bond pdb=" CB CYS R 336 " pdb=" SG CYS R 336 " ideal model delta sigma weight residual 1.808 1.716 0.092 3.30e-02 9.18e+02 7.73e+00 bond pdb=" CG1 ILE R 418 " pdb=" CD1 ILE R 418 " ideal model delta sigma weight residual 1.513 1.408 0.105 3.90e-02 6.57e+02 7.27e+00 bond pdb=" C PRO R 373 " pdb=" O PRO R 373 " ideal model delta sigma weight residual 1.235 1.206 0.029 1.30e-02 5.92e+03 5.12e+00 bond pdb=" CA CYS R 525 " pdb=" C CYS R 525 " ideal model delta sigma weight residual 1.527 1.548 -0.021 9.80e-03 1.04e+04 4.56e+00 bond pdb=" N LEU R 371 " pdb=" CA LEU R 371 " ideal model delta sigma weight residual 1.464 1.489 -0.025 1.20e-02 6.94e+03 4.33e+00 ... (remaining 3368 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 4250 2.26 - 4.52: 276 4.52 - 6.78: 51 6.78 - 9.04: 10 9.04 - 11.30: 6 Bond angle restraints: 4593 Sorted by residual: angle pdb=" N PRO R 373 " pdb=" CA PRO R 373 " pdb=" CB PRO R 373 " ideal model delta sigma weight residual 103.25 96.66 6.59 1.05e+00 9.07e-01 3.94e+01 angle pdb=" N ASN R 370 " pdb=" CA ASN R 370 " pdb=" C ASN R 370 " ideal model delta sigma weight residual 113.16 106.83 6.33 1.24e+00 6.50e-01 2.61e+01 angle pdb=" C ASP R 364 " pdb=" N TYR R 365 " pdb=" CA TYR R 365 " ideal model delta sigma weight residual 120.28 127.60 -7.32 1.44e+00 4.82e-01 2.58e+01 angle pdb=" C TYR B 50 " pdb=" N HIS B 51 " pdb=" CA HIS B 51 " ideal model delta sigma weight residual 121.54 130.77 -9.23 1.91e+00 2.74e-01 2.33e+01 angle pdb=" CB GLN R 409 " pdb=" CG GLN R 409 " pdb=" CD GLN R 409 " ideal model delta sigma weight residual 112.60 119.86 -7.26 1.70e+00 3.46e-01 1.82e+01 ... (remaining 4588 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.56: 1665 14.56 - 29.12: 241 29.12 - 43.68: 52 43.68 - 58.24: 10 58.24 - 72.80: 5 Dihedral angle restraints: 1973 sinusoidal: 769 harmonic: 1204 Sorted by residual: dihedral pdb=" CA LEU R 461 " pdb=" C LEU R 461 " pdb=" N LYS R 462 " pdb=" CA LYS R 462 " ideal model delta harmonic sigma weight residual 180.00 148.97 31.03 0 5.00e+00 4.00e-02 3.85e+01 dihedral pdb=" CA GLN B 80 " pdb=" C GLN B 80 " pdb=" N SER B 81 " pdb=" CA SER B 81 " ideal model delta harmonic sigma weight residual -180.00 -152.63 -27.37 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CB CYS R 336 " pdb=" SG CYS R 336 " pdb=" SG CYS R 361 " pdb=" CB CYS R 361 " ideal model delta sinusoidal sigma weight residual -86.00 -131.11 45.11 1 1.00e+01 1.00e-02 2.82e+01 ... (remaining 1970 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 320 0.059 - 0.118: 145 0.118 - 0.177: 39 0.177 - 0.235: 6 0.235 - 0.294: 2 Chirality restraints: 512 Sorted by residual: chirality pdb=" CB ILE R 468 " pdb=" CA ILE R 468 " pdb=" CG1 ILE R 468 " pdb=" CG2 ILE R 468 " both_signs ideal model delta sigma weight residual False 2.64 2.94 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CG LEU B 96 " pdb=" CB LEU B 96 " pdb=" CD1 LEU B 96 " pdb=" CD2 LEU B 96 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CG LEU B 48 " pdb=" CB LEU B 48 " pdb=" CD1 LEU B 48 " pdb=" CD2 LEU B 48 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 509 not shown) Planarity restraints: 589 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR R 365 " 0.013 2.00e-02 2.50e+03 2.82e-02 1.59e+01 pdb=" CG TYR R 365 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 TYR R 365 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR R 365 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR R 365 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR R 365 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR R 365 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR R 365 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR R 369 " -0.015 2.00e-02 2.50e+03 3.05e-02 9.31e+00 pdb=" C TYR R 369 " 0.053 2.00e-02 2.50e+03 pdb=" O TYR R 369 " -0.020 2.00e-02 2.50e+03 pdb=" N ASN R 370 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 88 " 0.017 2.00e-02 2.50e+03 2.05e-02 8.38e+00 pdb=" CG TYR B 88 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR B 88 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR B 88 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR B 88 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR B 88 " -0.013 2.00e-02 2.50e+03 pdb=" CZ TYR B 88 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 88 " -0.000 2.00e-02 2.50e+03 ... (remaining 586 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 824 2.78 - 3.31: 3092 3.31 - 3.84: 5780 3.84 - 4.37: 6424 4.37 - 4.90: 10952 Nonbonded interactions: 27072 Sorted by model distance: nonbonded pdb=" OG SER R 438 " pdb=" O LYS R 440 " model vdw 2.255 3.040 nonbonded pdb=" OG1 THR B 13 " pdb=" OE1 GLN B 16 " model vdw 2.260 3.040 nonbonded pdb=" O PRO B 7 " pdb=" OG1 THR B 105 " model vdw 2.284 3.040 nonbonded pdb=" OD2 ASP R 398 " pdb=" OH TYR R 423 " model vdw 2.304 3.040 nonbonded pdb=" O TYR R 396 " pdb=" OG SER R 514 " model vdw 2.307 3.040 ... (remaining 27067 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 3.930 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 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 : 0.009 0.105 3380 Z= 0.400 Angle : 1.325 11.297 4609 Z= 0.713 Chirality : 0.069 0.294 512 Planarity : 0.009 0.067 588 Dihedral : 14.139 72.801 1190 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.73 % Allowed : 11.46 % Favored : 87.80 % Rotamer: Outliers : 0.55 % Allowed : 1.38 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -2.57 (0.39), residues: 410 helix: -4.65 (0.52), residues: 21 sheet: -0.77 (0.43), residues: 142 loop : -2.08 (0.37), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG R 408 TYR 0.066 0.005 TYR R 365 PHE 0.034 0.004 PHE A 96 TRP 0.020 0.004 TRP A 55 HIS 0.011 0.003 HIS R 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00895 / 0.40 ( 3373) covalent geometry : angle 1.31559 / 0.71 ( 4593) SS BOND : bond 0.00546 / 0.32 ( 5) SS BOND : angle 3.26513 / 2.16 ( 10) hydrogen bonds : bond 0.28264 / 16.15 ( 77) hydrogen bonds : angle 11.83711 / 7.76 ( 174) link_BETA1-4 : bond 0.00189 / 0.10 ( 1) link_BETA1-4 : angle 3.48057 / 2.42 ( 3) link_NAG-ASN : bond 0.00592 / 0.31 ( 1) link_NAG-ASN : angle 1.14195 / 0.72 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 166 time to evaluate : 0.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 353 TRP cc_start: 0.8506 (p-90) cc_final: 0.7034 (p-90) REVERT: R 387 LEU cc_start: 0.8124 (mp) cc_final: 0.7595 (mp) REVERT: R 396 TYR cc_start: 0.6913 (m-80) cc_final: 0.6704 (m-80) REVERT: R 410 ILE cc_start: 0.8475 (mm) cc_final: 0.8253 (mm) REVERT: R 453 TYR cc_start: 0.7520 (p90) cc_final: 0.7298 (p90) REVERT: R 496 SER cc_start: 0.8448 (t) cc_final: 0.8172 (p) REVERT: A 4 LEU cc_start: 0.8974 (mm) cc_final: 0.8681 (mm) REVERT: A 7 SER cc_start: 0.9348 (p) cc_final: 0.8989 (m) REVERT: A 69 LEU cc_start: 0.8035 (mm) cc_final: 0.7822 (mm) REVERT: A 115 MET cc_start: 0.8302 (tpt) cc_final: 0.7835 (tpp) REVERT: A 121 MET cc_start: 0.6637 (ptt) cc_final: 0.6412 (ppp) REVERT: B 36 TRP cc_start: 0.8302 (m100) cc_final: 0.8069 (m100) REVERT: B 37 TYR cc_start: 0.7704 (m-80) cc_final: 0.7321 (m-80) REVERT: B 90 GLU cc_start: 0.8174 (pt0) cc_final: 0.6756 (pt0) REVERT: B 91 THR cc_start: 0.8922 (m) cc_final: 0.8605 (p) REVERT: B 101 PHE cc_start: 0.8501 (m-80) cc_final: 0.8252 (m-10) REVERT: B 109 VAL cc_start: 0.3809 (p) cc_final: 0.3385 (p) outliers start: 2 outliers final: 0 residues processed: 168 average time/residue: 0.0744 time to fit residues: 14.6598 Evaluate side-chains 102 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 0.0770 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 409 GLN ** R 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN B 38 GLN B 39 HIS ** B 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.133414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.115649 restraints weight = 8620.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.118952 restraints weight = 5153.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.121136 restraints weight = 3485.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.122772 restraints weight = 2593.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.123969 restraints weight = 2059.911| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 3380 Z= 0.189 Angle : 0.823 9.700 4609 Z= 0.424 Chirality : 0.048 0.210 512 Planarity : 0.008 0.123 588 Dihedral : 7.323 31.319 456 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.02 % Favored : 90.73 % Rotamer: Outliers : 0.28 % Allowed : 7.46 % Favored : 92.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -2.72 (0.38), residues: 410 helix: -4.56 (0.91), residues: 12 sheet: -1.10 (0.42), residues: 123 loop : -2.13 (0.35), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 355 TYR 0.015 0.002 TYR R 421 PHE 0.017 0.002 PHE R 377 TRP 0.023 0.003 TRP A 49 HIS 0.006 0.002 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.19 ( 3373) covalent geometry : angle 0.82060 / 0.42 ( 4593) SS BOND : bond 0.00326 / 0.16 ( 5) SS BOND : angle 1.26270 / 0.75 ( 10) hydrogen bonds : bond 0.04946 / 2.99 ( 77) hydrogen bonds : angle 8.61943 / 5.67 ( 174) link_BETA1-4 : bond 0.00149 / 0.08 ( 1) link_BETA1-4 : angle 2.01271 / 1.59 ( 3) link_NAG-ASN : bond 0.00086 / 0.05 ( 1) link_NAG-ASN : angle 0.94460 / 0.54 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 0.119 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 365 TYR cc_start: 0.7535 (m-80) cc_final: 0.7280 (m-80) REVERT: R 428 ASP cc_start: 0.7688 (t0) cc_final: 0.7167 (t0) REVERT: R 496 SER cc_start: 0.8457 (t) cc_final: 0.7877 (p) REVERT: A 4 LEU cc_start: 0.9047 (mm) cc_final: 0.8835 (mm) REVERT: A 7 SER cc_start: 0.9342 (p) cc_final: 0.9069 (m) REVERT: A 61 TYR cc_start: 0.6377 (m-80) cc_final: 0.6016 (m-80) REVERT: A 62 ASN cc_start: 0.9065 (t0) cc_final: 0.8646 (t0) REVERT: A 87 VAL cc_start: 0.8504 (t) cc_final: 0.8277 (p) REVERT: A 111 ASP cc_start: 0.9102 (t0) cc_final: 0.8830 (t0) REVERT: A 115 MET cc_start: 0.8167 (tpt) cc_final: 0.7954 (tpp) REVERT: B 91 THR cc_start: 0.8843 (m) cc_final: 0.8381 (p) REVERT: B 99 VAL cc_start: 0.9119 (t) cc_final: 0.8721 (t) REVERT: B 106 ARG cc_start: 0.8741 (mtm110) cc_final: 0.8408 (mtm-85) outliers start: 1 outliers final: 1 residues processed: 124 average time/residue: 0.0688 time to fit residues: 10.3605 Evaluate side-chains 95 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 15 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 9 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 334 ASN R 474 GLN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.131715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.114077 restraints weight = 8667.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.117184 restraints weight = 5244.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.119435 restraints weight = 3610.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.120985 restraints weight = 2697.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.122003 restraints weight = 2145.690| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 3380 Z= 0.185 Angle : 0.762 6.813 4609 Z= 0.395 Chirality : 0.047 0.172 512 Planarity : 0.007 0.106 588 Dihedral : 6.767 30.425 456 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.00 % Favored : 89.76 % Rotamer: Outliers : 0.28 % Allowed : 5.52 % Favored : 94.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -2.40 (0.40), residues: 410 helix: -4.81 (0.64), residues: 14 sheet: -1.05 (0.43), residues: 132 loop : -1.76 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 454 TYR 0.019 0.002 TYR B 50 PHE 0.019 0.002 PHE R 377 TRP 0.021 0.003 TRP A 49 HIS 0.004 0.002 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.19 ( 3373) covalent geometry : angle 0.75933 / 0.39 ( 4593) SS BOND : bond 0.00239 / 0.14 ( 5) SS BOND : angle 1.18836 / 0.72 ( 10) hydrogen bonds : bond 0.04064 / 2.45 ( 77) hydrogen bonds : angle 7.76595 / 5.10 ( 174) link_BETA1-4 : bond 0.00222 / 0.12 ( 1) link_BETA1-4 : angle 1.82903 / 1.66 ( 3) link_NAG-ASN : bond 0.00234 / 0.12 ( 1) link_NAG-ASN : angle 1.24643 / 0.71 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 0.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 428 ASP cc_start: 0.7883 (t0) cc_final: 0.7255 (t0) REVERT: R 474 GLN cc_start: 0.6181 (OUTLIER) cc_final: 0.5626 (tm-30) REVERT: A 7 SER cc_start: 0.9410 (p) cc_final: 0.9132 (m) REVERT: A 40 ARG cc_start: 0.8568 (tpp80) cc_final: 0.7966 (ttm-80) REVERT: A 61 TYR cc_start: 0.6458 (m-80) cc_final: 0.5769 (m-80) REVERT: A 62 ASN cc_start: 0.9056 (t0) cc_final: 0.8658 (t0) REVERT: A 111 ASP cc_start: 0.9089 (t0) cc_final: 0.8698 (t0) REVERT: B 90 GLU cc_start: 0.7708 (pt0) cc_final: 0.7314 (pt0) REVERT: B 99 VAL cc_start: 0.9134 (t) cc_final: 0.8690 (t) REVERT: B 106 ARG cc_start: 0.8722 (mtm110) cc_final: 0.8463 (mtm-85) outliers start: 1 outliers final: 0 residues processed: 120 average time/residue: 0.0645 time to fit residues: 9.5207 Evaluate side-chains 96 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 7 optimal weight: 0.0980 chunk 36 optimal weight: 4.9990 chunk 26 optimal weight: 0.1980 chunk 29 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 9 optimal weight: 0.3980 chunk 24 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 2 optimal weight: 0.5980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 417 ASN B 6 GLN B 38 GLN ** B 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.134566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.116883 restraints weight = 8339.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.120080 restraints weight = 5005.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.122313 restraints weight = 3416.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.123917 restraints weight = 2542.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.124922 restraints weight = 2012.700| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.4700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3380 Z= 0.137 Angle : 0.727 7.590 4609 Z= 0.367 Chirality : 0.046 0.200 512 Planarity : 0.007 0.110 588 Dihedral : 6.368 30.829 456 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.02 % Favored : 90.73 % Rotamer: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -2.14 (0.41), residues: 410 helix: -4.84 (0.62), residues: 14 sheet: -0.88 (0.45), residues: 131 loop : -1.56 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 408 TYR 0.017 0.001 TYR R 421 PHE 0.016 0.002 PHE R 377 TRP 0.028 0.003 TRP B 36 HIS 0.005 0.002 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 3373) covalent geometry : angle 0.71876 / 0.36 ( 4593) SS BOND : bond 0.00266 / 0.14 ( 5) SS BOND : angle 2.21672 / 1.19 ( 10) hydrogen bonds : bond 0.03585 / 2.23 ( 77) hydrogen bonds : angle 7.16619 / 4.73 ( 174) link_BETA1-4 : bond 0.00204 / 0.11 ( 1) link_BETA1-4 : angle 1.53090 / 1.27 ( 3) link_NAG-ASN : bond 0.00306 / 0.16 ( 1) link_NAG-ASN : angle 1.26914 / 0.72 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 428 ASP cc_start: 0.7840 (t0) cc_final: 0.7159 (t0) REVERT: R 500 THR cc_start: 0.8798 (p) cc_final: 0.8506 (p) REVERT: A 7 SER cc_start: 0.9395 (p) cc_final: 0.9121 (m) REVERT: A 13 LYS cc_start: 0.4328 (mmtt) cc_final: 0.3864 (mmmt) REVERT: A 61 TYR cc_start: 0.6664 (m-80) cc_final: 0.5953 (m-80) REVERT: A 62 ASN cc_start: 0.9004 (t0) cc_final: 0.8571 (t0) REVERT: B 37 TYR cc_start: 0.7652 (m-80) cc_final: 0.6504 (m-10) REVERT: B 49 ILE cc_start: 0.8122 (tp) cc_final: 0.7854 (tp) REVERT: B 90 GLU cc_start: 0.7835 (pt0) cc_final: 0.7478 (pt0) REVERT: B 99 VAL cc_start: 0.9131 (t) cc_final: 0.8549 (t) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.0634 time to fit residues: 9.9235 Evaluate side-chains 91 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.8980 chunk 28 optimal weight: 0.0980 chunk 36 optimal weight: 6.9990 chunk 20 optimal weight: 0.0770 chunk 24 optimal weight: 0.0050 chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 overall best weight: 0.6154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 417 ASN ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN ** B 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.132161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.114527 restraints weight = 8289.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.117685 restraints weight = 4932.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.119989 restraints weight = 3357.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.121301 restraints weight = 2487.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.122674 restraints weight = 2009.947| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.5119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3380 Z= 0.148 Angle : 0.717 6.829 4609 Z= 0.364 Chirality : 0.046 0.178 512 Planarity : 0.006 0.092 588 Dihedral : 6.226 30.325 456 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.76 % Favored : 90.00 % Rotamer: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -2.05 (0.42), residues: 410 helix: -3.79 (0.80), residues: 20 sheet: -0.85 (0.45), residues: 136 loop : -1.46 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 106 TYR 0.014 0.002 TYR R 423 PHE 0.019 0.002 PHE R 377 TRP 0.028 0.003 TRP B 36 HIS 0.004 0.001 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 3373) covalent geometry : angle 0.70703 / 0.36 ( 4593) SS BOND : bond 0.00165 / 0.09 ( 5) SS BOND : angle 2.33697 / 1.26 ( 10) hydrogen bonds : bond 0.03311 / 2.00 ( 77) hydrogen bonds : angle 6.94732 / 4.60 ( 174) link_BETA1-4 : bond 0.00062 / 0.03 ( 1) link_BETA1-4 : angle 1.57579 / 1.42 ( 3) link_NAG-ASN : bond 0.00380 / 0.20 ( 1) link_NAG-ASN : angle 1.68373 / 1.00 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 386 LYS cc_start: 0.7919 (pttt) cc_final: 0.7623 (pttp) REVERT: R 409 GLN cc_start: 0.8888 (mm110) cc_final: 0.8451 (mm-40) REVERT: R 428 ASP cc_start: 0.7946 (t0) cc_final: 0.7355 (t70) REVERT: R 500 THR cc_start: 0.8611 (p) cc_final: 0.8103 (t) REVERT: A 7 SER cc_start: 0.9406 (p) cc_final: 0.9097 (m) REVERT: A 61 TYR cc_start: 0.6787 (m-80) cc_final: 0.6108 (m-80) REVERT: A 62 ASN cc_start: 0.9021 (t0) cc_final: 0.8502 (t0) REVERT: B 36 TRP cc_start: 0.7888 (m100) cc_final: 0.7681 (m100) REVERT: B 37 TYR cc_start: 0.7704 (m-80) cc_final: 0.6051 (m-10) REVERT: B 48 LEU cc_start: 0.8814 (mt) cc_final: 0.8436 (mt) REVERT: B 49 ILE cc_start: 0.8129 (tp) cc_final: 0.7433 (tt) REVERT: B 90 GLU cc_start: 0.7796 (pt0) cc_final: 0.7473 (pt0) REVERT: B 99 VAL cc_start: 0.9134 (t) cc_final: 0.8585 (t) REVERT: B 106 ARG cc_start: 0.8557 (mtm-85) cc_final: 0.8354 (mtp85) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.0532 time to fit residues: 8.0297 Evaluate side-chains 91 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 16 optimal weight: 3.9990 chunk 19 optimal weight: 0.0040 chunk 35 optimal weight: 0.4980 chunk 14 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 1 optimal weight: 0.7980 chunk 37 optimal weight: 0.0980 overall best weight: 0.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN ** B 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 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 = 0.3908 r_free = 0.3908 target = 0.136594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.119138 restraints weight = 8531.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.122397 restraints weight = 5127.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.124707 restraints weight = 3479.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.126413 restraints weight = 2568.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.127479 restraints weight = 2014.525| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.5352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3380 Z= 0.124 Angle : 0.711 8.715 4609 Z= 0.359 Chirality : 0.046 0.184 512 Planarity : 0.007 0.115 588 Dihedral : 6.064 29.403 456 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.56 % Favored : 92.20 % Rotamer: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.43), residues: 410 helix: -3.68 (0.83), residues: 20 sheet: -0.85 (0.45), residues: 139 loop : -1.24 (0.42), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 457 TYR 0.009 0.001 TYR R 423 PHE 0.018 0.001 PHE R 377 TRP 0.021 0.002 TRP A 49 HIS 0.005 0.001 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 3373) covalent geometry : angle 0.70525 / 0.36 ( 4593) SS BOND : bond 0.00296 / 0.19 ( 5) SS BOND : angle 1.86299 / 1.02 ( 10) hydrogen bonds : bond 0.03197 / 1.98 ( 77) hydrogen bonds : angle 6.73700 / 4.48 ( 174) link_BETA1-4 : bond 0.00479 / 0.25 ( 1) link_BETA1-4 : angle 1.49053 / 1.27 ( 3) link_NAG-ASN : bond 0.00258 / 0.14 ( 1) link_NAG-ASN : angle 1.52139 / 0.87 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.137 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 386 LYS cc_start: 0.7834 (pttt) cc_final: 0.7526 (pttp) REVERT: R 409 GLN cc_start: 0.8939 (mm110) cc_final: 0.8423 (mm-40) REVERT: R 428 ASP cc_start: 0.7931 (t0) cc_final: 0.7364 (t70) REVERT: R 500 THR cc_start: 0.8613 (p) cc_final: 0.8051 (t) REVERT: A 7 SER cc_start: 0.9367 (p) cc_final: 0.9052 (m) REVERT: A 13 LYS cc_start: 0.4617 (mmtt) cc_final: 0.4203 (mmmt) REVERT: A 40 ARG cc_start: 0.8617 (tpp80) cc_final: 0.8186 (ttm-80) REVERT: A 61 TYR cc_start: 0.6774 (m-80) cc_final: 0.6483 (m-80) REVERT: B 39 HIS cc_start: 0.7416 (t70) cc_final: 0.7119 (t70) REVERT: B 48 LEU cc_start: 0.8978 (mt) cc_final: 0.8617 (mt) REVERT: B 93 ASP cc_start: 0.7003 (t0) cc_final: 0.6417 (t0) REVERT: B 106 ARG cc_start: 0.8607 (mtm-85) cc_final: 0.8301 (mtp180) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.0608 time to fit residues: 9.7571 Evaluate side-chains 100 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 29 optimal weight: 0.9980 chunk 21 optimal weight: 0.0970 chunk 11 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 2 optimal weight: 0.0770 chunk 28 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 7 optimal weight: 0.0670 chunk 0 optimal weight: 0.5980 overall best weight: 0.2674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN B 38 GLN ** B 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.136438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.118941 restraints weight = 8372.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.122257 restraints weight = 5016.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.124597 restraints weight = 3406.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.126267 restraints weight = 2502.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.127362 restraints weight = 1961.895| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.5517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3380 Z= 0.122 Angle : 0.715 7.660 4609 Z= 0.358 Chirality : 0.046 0.192 512 Planarity : 0.006 0.096 588 Dihedral : 6.060 30.536 456 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.29 % Favored : 91.46 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -1.94 (0.42), residues: 410 helix: -3.38 (0.98), residues: 20 sheet: -0.94 (0.44), residues: 141 loop : -1.32 (0.41), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 17 TYR 0.023 0.001 TYR B 50 PHE 0.022 0.001 PHE R 377 TRP 0.040 0.003 TRP B 36 HIS 0.005 0.001 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 3373) covalent geometry : angle 0.71366 / 0.36 ( 4593) SS BOND : bond 0.00348 / 0.19 ( 5) SS BOND : angle 0.87554 / 0.50 ( 10) hydrogen bonds : bond 0.03392 / 2.07 ( 77) hydrogen bonds : angle 6.53431 / 4.28 ( 174) link_BETA1-4 : bond 0.00221 / 0.12 ( 1) link_BETA1-4 : angle 1.34624 / 1.12 ( 3) link_NAG-ASN : bond 0.00289 / 0.15 ( 1) link_NAG-ASN : angle 1.51158 / 0.87 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 386 LYS cc_start: 0.7763 (pttt) cc_final: 0.7463 (pttp) REVERT: R 409 GLN cc_start: 0.9005 (mm110) cc_final: 0.8147 (mm-40) REVERT: R 428 ASP cc_start: 0.7817 (t0) cc_final: 0.7230 (t70) REVERT: R 498 ARG cc_start: 0.8347 (mtm110) cc_final: 0.7924 (ptp-170) REVERT: R 500 THR cc_start: 0.8560 (p) cc_final: 0.8174 (t) REVERT: A 7 SER cc_start: 0.9345 (p) cc_final: 0.9054 (m) REVERT: A 13 LYS cc_start: 0.4785 (mmtt) cc_final: 0.4415 (mmmt) REVERT: A 15 LYS cc_start: 0.8361 (tppt) cc_final: 0.8132 (tmmt) REVERT: A 40 ARG cc_start: 0.8532 (tpp80) cc_final: 0.8094 (ttm-80) REVERT: A 61 TYR cc_start: 0.6840 (m-80) cc_final: 0.6545 (m-80) REVERT: B 39 HIS cc_start: 0.7358 (t70) cc_final: 0.7095 (t70) REVERT: B 48 LEU cc_start: 0.8975 (mt) cc_final: 0.8505 (mt) REVERT: B 93 ASP cc_start: 0.7007 (t0) cc_final: 0.6515 (t0) REVERT: B 106 ARG cc_start: 0.8575 (mtm-85) cc_final: 0.8333 (mtp85) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.0669 time to fit residues: 10.2153 Evaluate side-chains 110 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 36 optimal weight: 6.9990 chunk 3 optimal weight: 0.0470 chunk 34 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 409 GLN ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN ** B 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.134044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.115910 restraints weight = 8553.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.119250 restraints weight = 5239.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.121594 restraints weight = 3594.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.123272 restraints weight = 2672.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.124352 restraints weight = 2108.467| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.5729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3380 Z= 0.144 Angle : 0.699 6.292 4609 Z= 0.356 Chirality : 0.046 0.181 512 Planarity : 0.006 0.088 588 Dihedral : 6.126 28.489 456 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.54 % Favored : 91.22 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % 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: -2.03 (0.42), residues: 410 helix: -3.67 (0.88), residues: 20 sheet: -1.02 (0.44), residues: 141 loop : -1.34 (0.41), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 454 TYR 0.010 0.001 TYR R 423 PHE 0.023 0.001 PHE R 377 TRP 0.048 0.003 TRP B 36 HIS 0.005 0.002 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 3373) covalent geometry : angle 0.69416 / 0.35 ( 4593) SS BOND : bond 0.00181 / 0.11 ( 5) SS BOND : angle 1.61388 / 0.96 ( 10) hydrogen bonds : bond 0.03376 / 2.09 ( 77) hydrogen bonds : angle 6.53317 / 4.27 ( 174) link_BETA1-4 : bond 0.00252 / 0.13 ( 1) link_BETA1-4 : angle 1.46223 / 1.26 ( 3) link_NAG-ASN : bond 0.00373 / 0.20 ( 1) link_NAG-ASN : angle 1.36880 / 0.78 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 386 LYS cc_start: 0.7940 (pttt) cc_final: 0.7657 (pttp) REVERT: R 428 ASP cc_start: 0.8037 (t0) cc_final: 0.7401 (t70) REVERT: R 498 ARG cc_start: 0.8369 (mtm110) cc_final: 0.7986 (ptp-170) REVERT: R 500 THR cc_start: 0.8666 (p) cc_final: 0.8258 (t) REVERT: A 7 SER cc_start: 0.9353 (p) cc_final: 0.9048 (m) REVERT: A 13 LYS cc_start: 0.4526 (mmtt) cc_final: 0.4137 (mmmt) REVERT: A 61 TYR cc_start: 0.6913 (m-80) cc_final: 0.6706 (m-80) REVERT: B 93 ASP cc_start: 0.7095 (t0) cc_final: 0.6751 (t0) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.0508 time to fit residues: 7.8389 Evaluate side-chains 102 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.4980 chunk 15 optimal weight: 0.0050 chunk 22 optimal weight: 2.9990 chunk 4 optimal weight: 0.0570 chunk 11 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 32 optimal weight: 0.1980 overall best weight: 0.2912 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN ** B 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 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 = 0.3904 r_free = 0.3904 target = 0.136635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.119155 restraints weight = 8516.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.122555 restraints weight = 5128.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.124960 restraints weight = 3451.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.126646 restraints weight = 2523.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.127907 restraints weight = 1963.341| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.5984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3380 Z= 0.129 Angle : 0.711 6.711 4609 Z= 0.360 Chirality : 0.046 0.182 512 Planarity : 0.006 0.084 588 Dihedral : 6.214 38.441 456 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.80 % Favored : 91.95 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -1.92 (0.42), residues: 410 helix: -3.69 (0.87), residues: 20 sheet: -0.79 (0.46), residues: 136 loop : -1.35 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG R 454 TYR 0.013 0.001 TYR B 37 PHE 0.023 0.001 PHE R 377 TRP 0.023 0.002 TRP B 36 HIS 0.005 0.002 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 3373) covalent geometry : angle 0.70444 / 0.36 ( 4593) SS BOND : bond 0.00293 / 0.17 ( 5) SS BOND : angle 2.02038 / 1.21 ( 10) hydrogen bonds : bond 0.03385 / 2.16 ( 77) hydrogen bonds : angle 6.42574 / 4.18 ( 174) link_BETA1-4 : bond 0.00124 / 0.07 ( 1) link_BETA1-4 : angle 1.34551 / 1.08 ( 3) link_NAG-ASN : bond 0.00308 / 0.16 ( 1) link_NAG-ASN : angle 1.41069 / 0.79 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 386 LYS cc_start: 0.7824 (pttt) cc_final: 0.7558 (pttp) REVERT: R 428 ASP cc_start: 0.8026 (t0) cc_final: 0.7387 (t70) REVERT: R 500 THR cc_start: 0.8654 (p) cc_final: 0.8140 (t) REVERT: A 7 SER cc_start: 0.9342 (p) cc_final: 0.9037 (m) REVERT: A 13 LYS cc_start: 0.4694 (mmtt) cc_final: 0.4352 (mmmt) REVERT: A 61 TYR cc_start: 0.6897 (m-80) cc_final: 0.6646 (m-80) REVERT: B 90 GLU cc_start: 0.7915 (pt0) cc_final: 0.7597 (pt0) REVERT: B 93 ASP cc_start: 0.7110 (t0) cc_final: 0.6793 (t0) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.0557 time to fit residues: 9.0349 Evaluate side-chains 108 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 17 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 36 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 30 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 chunk 22 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN ** B 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 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 = 0.3883 r_free = 0.3883 target = 0.134465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.117201 restraints weight = 8616.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.120594 restraints weight = 5155.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.122967 restraints weight = 3499.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.124492 restraints weight = 2569.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.125741 restraints weight = 2028.742| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.6134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3380 Z= 0.160 Angle : 0.756 6.008 4609 Z= 0.384 Chirality : 0.047 0.178 512 Planarity : 0.006 0.082 588 Dihedral : 6.370 32.437 456 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.76 % Favored : 90.00 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -2.04 (0.42), residues: 410 helix: -3.79 (0.84), residues: 20 sheet: -0.90 (0.46), residues: 134 loop : -1.41 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 454 TYR 0.014 0.002 TYR R 380 PHE 0.016 0.002 PHE R 377 TRP 0.058 0.003 TRP B 36 HIS 0.004 0.002 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 ( 3373) covalent geometry : angle 0.74700 / 0.38 ( 4593) SS BOND : bond 0.00261 / 0.14 ( 5) SS BOND : angle 2.42794 / 1.50 ( 10) hydrogen bonds : bond 0.03375 / 2.14 ( 77) hydrogen bonds : angle 6.36740 / 4.11 ( 174) link_BETA1-4 : bond 0.00155 / 0.08 ( 1) link_BETA1-4 : angle 1.42584 / 1.24 ( 3) link_NAG-ASN : bond 0.00368 / 0.19 ( 1) link_NAG-ASN : angle 1.22241 / 0.71 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 386 LYS cc_start: 0.7808 (pttt) cc_final: 0.7536 (pttp) REVERT: R 428 ASP cc_start: 0.8072 (t0) cc_final: 0.7492 (t70) REVERT: R 500 THR cc_start: 0.8687 (p) cc_final: 0.8180 (t) REVERT: A 7 SER cc_start: 0.9371 (p) cc_final: 0.8983 (m) REVERT: A 13 LYS cc_start: 0.4789 (mmtt) cc_final: 0.4358 (mmmt) REVERT: A 61 TYR cc_start: 0.6868 (m-80) cc_final: 0.6619 (m-80) REVERT: A 66 LYS cc_start: 0.8640 (mmmt) cc_final: 0.8372 (tppp) REVERT: A 97 CYS cc_start: 0.5303 (p) cc_final: 0.5083 (p) REVERT: B 90 GLU cc_start: 0.8076 (pt0) cc_final: 0.7848 (pt0) REVERT: B 93 ASP cc_start: 0.7075 (t0) cc_final: 0.6742 (t0) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.0522 time to fit residues: 8.3429 Evaluate side-chains 103 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 34 optimal weight: 0.6980 chunk 14 optimal weight: 0.0370 chunk 8 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 chunk 37 optimal weight: 0.3980 chunk 3 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 0.0030 chunk 22 optimal weight: 0.1980 chunk 27 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.2668 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN ** B 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 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 = 0.3896 r_free = 0.3896 target = 0.135883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.118345 restraints weight = 9052.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.121724 restraints weight = 5433.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.124168 restraints weight = 3685.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.125679 restraints weight = 2700.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.126838 restraints weight = 2135.642| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.6336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 3380 Z= 0.128 Angle : 0.742 10.896 4609 Z= 0.371 Chirality : 0.047 0.181 512 Planarity : 0.006 0.080 588 Dihedral : 6.251 30.777 456 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.24 % Favored : 89.51 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.51 % 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: -1.96 (0.42), residues: 410 helix: -3.92 (0.79), residues: 20 sheet: -0.72 (0.46), residues: 130 loop : -1.43 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG R 454 TYR 0.028 0.002 TYR B 50 PHE 0.018 0.001 PHE R 377 TRP 0.026 0.003 TRP A 49 HIS 0.005 0.001 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 3373) covalent geometry : angle 0.73342 / 0.37 ( 4593) SS BOND : bond 0.00745 / 0.39 ( 5) SS BOND : angle 2.39211 / 1.60 ( 10) hydrogen bonds : bond 0.03324 / 2.12 ( 77) hydrogen bonds : angle 6.20333 / 4.03 ( 174) link_BETA1-4 : bond 0.00309 / 0.16 ( 1) link_BETA1-4 : angle 1.29474 / 1.08 ( 3) link_NAG-ASN : bond 0.00288 / 0.15 ( 1) link_NAG-ASN : angle 1.37190 / 0.77 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 887.60 seconds wall clock time: 15 minutes 59.36 seconds (959.36 seconds total)