Starting phenix.real_space_refine on Wed Jul 1 22:12:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7e3b_30978/07_2026/7e3b_30978.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e3b_30978/07_2026/7e3b_30978.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7e3b_30978/07_2026/7e3b_30978.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e3b_30978/07_2026/7e3b_30978.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7e3b_30978/07_2026/7e3b_30978.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7e3b_30978/07_2026/7e3b_30978.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7e3b_30978/07_2026/7e3b_30978.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e3b_30978/07_2026/7e3b_30978.map" } resolution = 4.2 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= 0.001 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 2095 2.51 5 N 541 2.21 5 O 649 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 3299 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "B" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 941 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "C" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 808 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 98} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 0.98, per 1000 atoms: 0.30 Number of scatterers: 3299 At special positions: 0 Unit cell: (68.481, 85.873, 72.829, 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 649 8.00 N 541 7.00 C 2095 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " 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 NAG-ASN " NAG A 601 " - " ASN A 343 " Time building additional restraints: 0.26 Conformation dependent library (CDL) restraints added in 121.3 milliseconds 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 770 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 9 sheets defined 11.6% alpha, 29.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.331A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 removed outlier: 4.364A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.136A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'B' and resid 61 through 64 Processing helix chain 'B' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'B' and resid 11 through 12 removed outlier: 3.561A pdb=" N SER B 35 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 5 through 6 Processing sheet with id=AA7, first strand: chain 'C' and resid 10 through 11 Processing sheet with id=AA8, first strand: chain 'C' and resid 10 through 11 removed outlier: 3.918A pdb=" N THR C 97 " --> pdb=" O GLN C 90 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 48 through 49 111 hydrogen bonds defined for protein. 255 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: 0.44 Time building geometry restraints manager: 0.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 1049 1.35 - 1.48: 968 1.48 - 1.60: 1352 1.60 - 1.73: 0 1.73 - 1.85: 16 Bond restraints: 3385 Sorted by residual: bond pdb=" CB PHE B 78 " pdb=" CG PHE B 78 " ideal model delta sigma weight residual 1.502 1.454 0.048 2.30e-02 1.89e+03 4.40e+00 bond pdb=" N TRP B 112 " pdb=" CA TRP B 112 " ideal model delta sigma weight residual 1.457 1.479 -0.022 1.29e-02 6.01e+03 2.88e+00 bond pdb=" CD2 PHE B 78 " pdb=" CE2 PHE B 78 " ideal model delta sigma weight residual 1.382 1.338 0.044 3.00e-02 1.11e+03 2.14e+00 bond pdb=" CB TRP B 112 " pdb=" CG TRP B 112 " ideal model delta sigma weight residual 1.498 1.453 0.045 3.10e-02 1.04e+03 2.12e+00 bond pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " ideal model delta sigma weight residual 1.808 1.854 -0.046 3.30e-02 9.18e+02 1.97e+00 ... (remaining 3380 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 4473 2.09 - 4.17: 117 4.17 - 6.26: 17 6.26 - 8.35: 2 8.35 - 10.44: 1 Bond angle restraints: 4610 Sorted by residual: angle pdb=" CA CYS A 432 " pdb=" CB CYS A 432 " pdb=" SG CYS A 432 " ideal model delta sigma weight residual 114.40 124.84 -10.44 2.30e+00 1.89e-01 2.06e+01 angle pdb=" CB LYS B 13 " pdb=" CG LYS B 13 " pdb=" CD LYS B 13 " ideal model delta sigma weight residual 111.30 118.65 -7.35 2.30e+00 1.89e-01 1.02e+01 angle pdb=" C ILE C 83 " pdb=" N ALA C 84 " pdb=" CA ALA C 84 " ideal model delta sigma weight residual 122.09 116.48 5.61 1.86e+00 2.89e-01 9.11e+00 angle pdb=" N CYS A 432 " pdb=" CA CYS A 432 " pdb=" C CYS A 432 " ideal model delta sigma weight residual 108.60 112.87 -4.27 1.46e+00 4.69e-01 8.54e+00 angle pdb=" C GLY A 431 " pdb=" N CYS A 432 " pdb=" CA CYS A 432 " ideal model delta sigma weight residual 121.80 116.95 4.85 1.71e+00 3.42e-01 8.04e+00 ... (remaining 4605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.19: 1797 17.19 - 34.37: 145 34.37 - 51.56: 24 51.56 - 68.74: 7 68.74 - 85.92: 3 Dihedral angle restraints: 1976 sinusoidal: 758 harmonic: 1218 Sorted by residual: dihedral pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " pdb=" SG CYS A 432 " pdb=" CB CYS A 432 " ideal model delta sinusoidal sigma weight residual 93.00 37.09 55.91 1 1.00e+01 1.00e-02 4.22e+01 dihedral pdb=" CA CYS A 432 " pdb=" C CYS A 432 " pdb=" N VAL A 433 " pdb=" CA VAL A 433 " ideal model delta harmonic sigma weight residual -180.00 -154.54 -25.46 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA ASP B 110 " pdb=" C ASP B 110 " pdb=" N ILE B 111 " pdb=" CA ILE B 111 " ideal model delta harmonic sigma weight residual -180.00 -158.89 -21.11 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 1973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 280 0.033 - 0.066: 146 0.066 - 0.099: 41 0.099 - 0.132: 23 0.132 - 0.165: 10 Chirality restraints: 500 Sorted by residual: chirality pdb=" CA ILE C 29 " pdb=" N ILE C 29 " pdb=" C ILE C 29 " pdb=" CB ILE C 29 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.81e-01 chirality pdb=" CA CYS A 432 " pdb=" N CYS A 432 " pdb=" C CYS A 432 " pdb=" CB CYS A 432 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.56e-01 chirality pdb=" CB ILE B 111 " pdb=" CA ILE B 111 " pdb=" CG1 ILE B 111 " pdb=" CG2 ILE B 111 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.15 2.00e-01 2.50e+01 5.92e-01 ... (remaining 497 not shown) Planarity restraints: 595 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 34 " -0.025 2.00e-02 2.50e+03 1.61e-02 6.50e+00 pdb=" CG TRP B 34 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP B 34 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP B 34 " 0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP B 34 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 34 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 34 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 34 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 34 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 34 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 8 " 0.027 5.00e-02 4.00e+02 4.06e-02 2.63e+00 pdb=" N PRO B 9 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 9 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 9 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 78 " 0.008 2.00e-02 2.50e+03 1.55e-02 2.40e+00 pdb=" C PHE B 78 " -0.027 2.00e-02 2.50e+03 pdb=" O PHE B 78 " 0.010 2.00e-02 2.50e+03 pdb=" N SER B 79 " 0.009 2.00e-02 2.50e+03 ... (remaining 592 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 746 2.77 - 3.30: 3195 3.30 - 3.84: 5475 3.84 - 4.37: 6437 4.37 - 4.90: 11064 Nonbonded interactions: 26917 Sorted by model distance: nonbonded pdb=" OD1 ASP B 98 " pdb=" N ARG B 99 " model vdw 2.241 3.120 nonbonded pdb=" NH2 ARG A 346 " pdb=" OD2 ASP B 98 " model vdw 2.250 3.120 nonbonded pdb=" OD1 ASN A 450 " pdb=" OH TYR B 50 " model vdw 2.275 3.040 nonbonded pdb=" NH2 ARG A 454 " pdb=" O SER A 469 " model vdw 2.290 3.120 nonbonded pdb=" NH1 ARG C 18 " pdb=" OG1 THR C 20 " model vdw 2.296 3.120 ... (remaining 26912 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: 2.280 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: 0.020 Process input model: 5.060 Find NCS groups from input model: 0.010 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: 8.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 3392 Z= 0.277 Angle : 0.817 10.437 4625 Z= 0.461 Chirality : 0.049 0.165 500 Planarity : 0.004 0.041 594 Dihedral : 13.280 85.922 1188 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.04 (0.38), residues: 415 helix: -3.08 (0.86), residues: 26 sheet: -1.07 (0.45), residues: 130 loop : -1.32 (0.35), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 61 TYR 0.022 0.002 TYR A 365 PHE 0.019 0.002 PHE B 78 TRP 0.040 0.003 TRP B 34 HIS 0.001 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00607 / 0.28 ( 3385) covalent geometry : angle 0.80991 / 0.46 ( 4610) SS BOND : bond 0.00891 / 0.44 ( 6) SS BOND : angle 2.23094 / 1.08 ( 12) hydrogen bonds : bond 0.17338 / 10.95 ( 106) hydrogen bonds : angle 8.91532 / 6.16 ( 255) link_NAG-ASN : bond 0.00075 / 0.04 ( 1) link_NAG-ASN : angle 1.27390 / 0.75 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.125 Fit side-chains REVERT: A 467 ASP cc_start: 0.8499 (t70) cc_final: 0.8014 (p0) REVERT: B 89 ASP cc_start: 0.9199 (m-30) cc_final: 0.8903 (m-30) REVERT: B 110 ASP cc_start: 0.8839 (t0) cc_final: 0.8567 (t0) REVERT: C 83 ILE cc_start: 0.9384 (mt) cc_final: 0.9178 (tt) REVERT: C 88 CYS cc_start: 0.6455 (p) cc_final: 0.6036 (p) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.0637 time to fit residues: 6.6609 Evaluate side-chains 76 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.8980 chunk 26 optimal weight: 0.3980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.070360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.056859 restraints weight = 8794.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.058834 restraints weight = 5007.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.060117 restraints weight = 3437.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.061094 restraints weight = 2670.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.061776 restraints weight = 2219.344| |-----------------------------------------------------------------------------| r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 3392 Z= 0.186 Angle : 0.657 10.356 4625 Z= 0.349 Chirality : 0.047 0.162 500 Planarity : 0.004 0.033 594 Dihedral : 5.226 23.665 464 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.66 (0.40), residues: 415 helix: -2.30 (0.87), residues: 27 sheet: -0.70 (0.47), residues: 130 loop : -1.18 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 61 TYR 0.022 0.002 TYR B 53 PHE 0.015 0.001 PHE B 78 TRP 0.024 0.002 TRP B 34 HIS 0.001 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 ( 3385) covalent geometry : angle 0.64944 / 0.35 ( 4610) SS BOND : bond 0.00814 / 0.39 ( 6) SS BOND : angle 2.02278 / 1.00 ( 12) hydrogen bonds : bond 0.03862 / 2.45 ( 106) hydrogen bonds : angle 7.17975 / 4.88 ( 255) link_NAG-ASN : bond 0.00092 / 0.05 ( 1) link_NAG-ASN : angle 1.29855 / 0.76 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.109 Fit side-chains REVERT: A 467 ASP cc_start: 0.8493 (t70) cc_final: 0.8012 (p0) REVERT: B 2 VAL cc_start: 0.9201 (t) cc_final: 0.8970 (t) REVERT: B 53 TYR cc_start: 0.8705 (p90) cc_final: 0.8284 (p90) REVERT: B 110 ASP cc_start: 0.8893 (t0) cc_final: 0.8621 (t0) REVERT: C 24 GLN cc_start: 0.8491 (tm-30) cc_final: 0.8228 (tm-30) REVERT: C 49 TYR cc_start: 0.8481 (p90) cc_final: 0.8212 (p90) REVERT: C 61 ARG cc_start: 0.8342 (ptp90) cc_final: 0.8065 (ptp90) REVERT: C 81 GLU cc_start: 0.8660 (pp20) cc_final: 0.8454 (pp20) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.0720 time to fit residues: 8.2816 Evaluate side-chains 82 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 35 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 30 optimal weight: 0.2980 chunk 13 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.071506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.057965 restraints weight = 8389.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.059826 restraints weight = 4903.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.061215 restraints weight = 3432.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.062132 restraints weight = 2650.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.062877 restraints weight = 2219.645| |-----------------------------------------------------------------------------| r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3392 Z= 0.179 Angle : 0.645 10.303 4625 Z= 0.338 Chirality : 0.047 0.190 500 Planarity : 0.004 0.034 594 Dihedral : 4.998 23.646 464 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.59 (0.40), residues: 415 helix: -2.34 (0.85), residues: 27 sheet: -0.55 (0.48), residues: 130 loop : -1.19 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 466 TYR 0.015 0.001 TYR B 53 PHE 0.011 0.001 PHE B 78 TRP 0.015 0.002 TRP B 34 HIS 0.001 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 ( 3385) covalent geometry : angle 0.63723 / 0.33 ( 4610) SS BOND : bond 0.00904 / 0.45 ( 6) SS BOND : angle 1.97393 / 1.01 ( 12) hydrogen bonds : bond 0.03485 / 2.22 ( 106) hydrogen bonds : angle 6.84747 / 4.64 ( 255) link_NAG-ASN : bond 0.00038 / 0.02 ( 1) link_NAG-ASN : angle 1.26847 / 0.74 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.129 Fit side-chains REVERT: A 467 ASP cc_start: 0.8480 (t70) cc_final: 0.7978 (p0) REVERT: B 2 VAL cc_start: 0.9182 (t) cc_final: 0.8957 (t) REVERT: B 48 ILE cc_start: 0.9605 (mt) cc_final: 0.9397 (mp) REVERT: B 53 TYR cc_start: 0.8694 (p90) cc_final: 0.8319 (p90) REVERT: B 110 ASP cc_start: 0.8865 (t0) cc_final: 0.8617 (t0) REVERT: C 24 GLN cc_start: 0.8426 (tm-30) cc_final: 0.8145 (tm-30) REVERT: C 49 TYR cc_start: 0.8516 (p90) cc_final: 0.8248 (p90) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.0687 time to fit residues: 8.2601 Evaluate side-chains 82 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 9 optimal weight: 0.2980 chunk 5 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.072231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.058558 restraints weight = 8477.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.060595 restraints weight = 4932.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.061914 restraints weight = 3405.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.063012 restraints weight = 2640.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.063772 restraints weight = 2152.152| |-----------------------------------------------------------------------------| r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3392 Z= 0.177 Angle : 0.637 10.478 4625 Z= 0.334 Chirality : 0.047 0.206 500 Planarity : 0.004 0.034 594 Dihedral : 4.927 22.954 464 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.55 (0.40), residues: 415 helix: -2.37 (0.86), residues: 27 sheet: -0.48 (0.48), residues: 130 loop : -1.17 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 466 TYR 0.018 0.002 TYR B 52 PHE 0.023 0.002 PHE B 78 TRP 0.022 0.002 TRP B 34 HIS 0.001 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 ( 3385) covalent geometry : angle 0.62945 / 0.33 ( 4610) SS BOND : bond 0.00837 / 0.41 ( 6) SS BOND : angle 1.94574 / 0.98 ( 12) hydrogen bonds : bond 0.03295 / 2.10 ( 106) hydrogen bonds : angle 6.70162 / 4.54 ( 255) link_NAG-ASN : bond 0.00000 / 0.00 ( 1) link_NAG-ASN : angle 1.21004 / 0.70 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.130 Fit side-chains REVERT: A 467 ASP cc_start: 0.8439 (t70) cc_final: 0.7888 (p0) REVERT: B 48 ILE cc_start: 0.9598 (mt) cc_final: 0.9349 (mp) REVERT: B 53 TYR cc_start: 0.8777 (p90) cc_final: 0.8413 (p90) REVERT: C 23 CYS cc_start: 0.5295 (t) cc_final: 0.4934 (t) REVERT: C 24 GLN cc_start: 0.8505 (tm-30) cc_final: 0.8156 (tm-30) REVERT: C 81 GLU cc_start: 0.8710 (pp20) cc_final: 0.8506 (pp20) REVERT: C 82 ASP cc_start: 0.8678 (m-30) cc_final: 0.8179 (m-30) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.0635 time to fit residues: 7.7387 Evaluate side-chains 82 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 8 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 33 optimal weight: 0.0030 chunk 11 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 26 optimal weight: 0.0970 chunk 30 optimal weight: 0.0670 chunk 40 optimal weight: 0.7980 overall best weight: 0.2926 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.073737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.060566 restraints weight = 8425.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.062623 restraints weight = 4837.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.064073 restraints weight = 3295.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.065002 restraints weight = 2495.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.065789 restraints weight = 2070.142| |-----------------------------------------------------------------------------| r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 3392 Z= 0.123 Angle : 0.634 10.162 4625 Z= 0.325 Chirality : 0.047 0.218 500 Planarity : 0.004 0.043 594 Dihedral : 4.673 21.327 464 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.44 (0.40), residues: 415 helix: -2.19 (0.92), residues: 27 sheet: -0.47 (0.49), residues: 132 loop : -1.07 (0.36), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 466 TYR 0.010 0.001 TYR B 53 PHE 0.021 0.002 PHE B 78 TRP 0.015 0.002 TRP B 112 HIS 0.001 0.000 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 3385) covalent geometry : angle 0.62785 / 0.32 ( 4610) SS BOND : bond 0.00782 / 0.38 ( 6) SS BOND : angle 1.83157 / 0.92 ( 12) hydrogen bonds : bond 0.03066 / 1.97 ( 106) hydrogen bonds : angle 6.42165 / 4.35 ( 255) link_NAG-ASN : bond 0.00135 / 0.07 ( 1) link_NAG-ASN : angle 1.06680 / 0.61 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.126 Fit side-chains REVERT: A 452 LEU cc_start: 0.9494 (mt) cc_final: 0.9253 (mt) REVERT: A 467 ASP cc_start: 0.8423 (t70) cc_final: 0.7879 (p0) REVERT: B 2 VAL cc_start: 0.9132 (t) cc_final: 0.8847 (t) REVERT: B 48 ILE cc_start: 0.9607 (mt) cc_final: 0.9370 (mp) REVERT: B 53 TYR cc_start: 0.8617 (p90) cc_final: 0.8353 (p90) REVERT: C 23 CYS cc_start: 0.5160 (t) cc_final: 0.4044 (t) REVERT: C 24 GLN cc_start: 0.8445 (tm-30) cc_final: 0.8162 (tm-30) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.0696 time to fit residues: 8.5501 Evaluate side-chains 80 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 26 optimal weight: 0.3980 chunk 30 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.071404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.058444 restraints weight = 8626.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.060358 restraints weight = 5123.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.061626 restraints weight = 3555.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.062627 restraints weight = 2767.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.063330 restraints weight = 2289.386| |-----------------------------------------------------------------------------| r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3392 Z= 0.177 Angle : 0.642 10.067 4625 Z= 0.333 Chirality : 0.047 0.233 500 Planarity : 0.004 0.034 594 Dihedral : 4.766 23.041 464 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.40 (0.40), residues: 415 helix: -2.09 (0.96), residues: 27 sheet: -0.46 (0.48), residues: 132 loop : -1.04 (0.36), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 466 TYR 0.010 0.001 TYR B 52 PHE 0.019 0.001 PHE B 78 TRP 0.009 0.002 TRP B 105 HIS 0.001 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 ( 3385) covalent geometry : angle 0.63510 / 0.33 ( 4610) SS BOND : bond 0.00803 / 0.39 ( 6) SS BOND : angle 1.84026 / 0.93 ( 12) hydrogen bonds : bond 0.03238 / 2.06 ( 106) hydrogen bonds : angle 6.30314 / 4.26 ( 255) link_NAG-ASN : bond 0.00000 / 0.00 ( 1) link_NAG-ASN : angle 1.21307 / 0.70 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.136 Fit side-chains REVERT: A 467 ASP cc_start: 0.8423 (t70) cc_final: 0.7878 (p0) REVERT: A 525 CYS cc_start: 0.6388 (m) cc_final: 0.6143 (m) REVERT: B 2 VAL cc_start: 0.9122 (t) cc_final: 0.8852 (t) REVERT: B 48 ILE cc_start: 0.9560 (mt) cc_final: 0.9347 (mp) REVERT: B 53 TYR cc_start: 0.8602 (p90) cc_final: 0.8295 (p90) REVERT: C 24 GLN cc_start: 0.8454 (tm-30) cc_final: 0.8228 (tm-30) REVERT: C 88 CYS cc_start: 0.5951 (p) cc_final: 0.5704 (p) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.0617 time to fit residues: 7.2491 Evaluate side-chains 81 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.3980 chunk 15 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 29 optimal weight: 0.2980 chunk 5 optimal weight: 0.3980 chunk 6 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.072149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.058668 restraints weight = 8762.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.060697 restraints weight = 5111.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.062046 restraints weight = 3526.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.062967 restraints weight = 2736.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.063728 restraints weight = 2280.978| |-----------------------------------------------------------------------------| r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3392 Z= 0.147 Angle : 0.684 9.807 4625 Z= 0.342 Chirality : 0.048 0.248 500 Planarity : 0.004 0.034 594 Dihedral : 4.711 22.404 464 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.38 (0.40), residues: 415 helix: -2.26 (0.97), residues: 27 sheet: -0.36 (0.48), residues: 132 loop : -1.06 (0.35), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 61 TYR 0.009 0.001 TYR B 53 PHE 0.017 0.001 PHE B 78 TRP 0.010 0.002 TRP B 112 HIS 0.001 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 ( 3385) covalent geometry : angle 0.67728 / 0.34 ( 4610) SS BOND : bond 0.00806 / 0.40 ( 6) SS BOND : angle 1.88362 / 0.98 ( 12) hydrogen bonds : bond 0.03125 / 1.98 ( 106) hydrogen bonds : angle 6.28443 / 4.27 ( 255) link_NAG-ASN : bond 0.00081 / 0.04 ( 1) link_NAG-ASN : angle 1.13782 / 0.65 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.132 Fit side-chains revert: symmetry clash REVERT: A 467 ASP cc_start: 0.8406 (t70) cc_final: 0.7856 (p0) REVERT: B 2 VAL cc_start: 0.9107 (t) cc_final: 0.8822 (t) REVERT: B 48 ILE cc_start: 0.9550 (mt) cc_final: 0.9319 (mp) REVERT: B 53 TYR cc_start: 0.8597 (p90) cc_final: 0.8353 (p90) REVERT: C 24 GLN cc_start: 0.8481 (tm-30) cc_final: 0.8206 (tm-30) REVERT: C 36 TYR cc_start: 0.8850 (m-10) cc_final: 0.8311 (m-80) REVERT: C 46 LEU cc_start: 0.9352 (tt) cc_final: 0.9151 (tt) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.0611 time to fit residues: 7.1824 Evaluate side-chains 85 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 33 optimal weight: 0.9990 chunk 32 optimal weight: 0.0980 chunk 28 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 5 optimal weight: 0.0060 chunk 0 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 17 optimal weight: 0.0050 overall best weight: 0.2610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.074286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.061084 restraints weight = 8737.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.063165 restraints weight = 4974.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.064553 restraints weight = 3374.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.065569 restraints weight = 2587.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.066376 restraints weight = 2123.382| |-----------------------------------------------------------------------------| r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3392 Z= 0.118 Angle : 0.664 9.432 4625 Z= 0.337 Chirality : 0.048 0.254 500 Planarity : 0.004 0.034 594 Dihedral : 4.600 21.514 464 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.34 (0.40), residues: 415 helix: -2.25 (0.98), residues: 27 sheet: -0.28 (0.48), residues: 132 loop : -1.07 (0.35), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 466 TYR 0.025 0.001 TYR B 52 PHE 0.017 0.001 PHE B 78 TRP 0.013 0.002 TRP B 112 HIS 0.001 0.000 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 3385) covalent geometry : angle 0.65922 / 0.34 ( 4610) SS BOND : bond 0.00756 / 0.37 ( 6) SS BOND : angle 1.64251 / 0.81 ( 12) hydrogen bonds : bond 0.03049 / 1.95 ( 106) hydrogen bonds : angle 6.18902 / 4.21 ( 255) link_NAG-ASN : bond 0.00140 / 0.07 ( 1) link_NAG-ASN : angle 1.02196 / 0.58 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.125 Fit side-chains REVERT: A 467 ASP cc_start: 0.8371 (t70) cc_final: 0.7845 (p0) REVERT: B 2 VAL cc_start: 0.9067 (t) cc_final: 0.8790 (t) REVERT: B 81 LYS cc_start: 0.9243 (mmtm) cc_final: 0.8995 (mptt) REVERT: B 120 VAL cc_start: 0.7998 (p) cc_final: 0.7407 (p) REVERT: C 24 GLN cc_start: 0.8442 (tm-30) cc_final: 0.8173 (tm-30) REVERT: C 36 TYR cc_start: 0.8828 (m-10) cc_final: 0.8212 (m-80) REVERT: C 78 LEU cc_start: 0.8915 (tt) cc_final: 0.8640 (tt) REVERT: C 79 GLN cc_start: 0.8731 (mm-40) cc_final: 0.8452 (mm-40) REVERT: C 88 CYS cc_start: 0.5596 (p) cc_final: 0.4897 (p) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.0640 time to fit residues: 7.3493 Evaluate side-chains 81 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 8 optimal weight: 0.0870 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.4980 chunk 5 optimal weight: 0.6980 chunk 29 optimal weight: 0.3980 chunk 15 optimal weight: 0.0470 chunk 9 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.3256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.073949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.060694 restraints weight = 8644.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.062701 restraints weight = 4949.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.064158 restraints weight = 3411.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.065149 restraints weight = 2601.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.065894 restraints weight = 2150.972| |-----------------------------------------------------------------------------| r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3392 Z= 0.122 Angle : 0.641 9.129 4625 Z= 0.326 Chirality : 0.047 0.251 500 Planarity : 0.004 0.034 594 Dihedral : 4.519 21.830 464 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.21 (0.40), residues: 415 helix: -2.28 (0.97), residues: 27 sheet: -0.15 (0.49), residues: 132 loop : -0.99 (0.36), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 466 TYR 0.022 0.001 TYR B 53 PHE 0.017 0.001 PHE B 78 TRP 0.015 0.002 TRP B 112 HIS 0.001 0.000 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 ( 3385) covalent geometry : angle 0.63574 / 0.32 ( 4610) SS BOND : bond 0.00721 / 0.35 ( 6) SS BOND : angle 1.73336 / 0.90 ( 12) hydrogen bonds : bond 0.03003 / 1.90 ( 106) hydrogen bonds : angle 6.12298 / 4.15 ( 255) link_NAG-ASN : bond 0.00113 / 0.06 ( 1) link_NAG-ASN : angle 1.02925 / 0.58 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.079 Fit side-chains revert: symmetry clash REVERT: A 467 ASP cc_start: 0.8362 (t70) cc_final: 0.7847 (p0) REVERT: B 2 VAL cc_start: 0.9046 (t) cc_final: 0.8759 (t) REVERT: B 120 VAL cc_start: 0.7576 (p) cc_final: 0.7262 (p) REVERT: C 24 GLN cc_start: 0.8498 (tm-30) cc_final: 0.8104 (tm-30) REVERT: C 36 TYR cc_start: 0.8780 (m-10) cc_final: 0.8269 (m-80) REVERT: C 78 LEU cc_start: 0.8919 (tt) cc_final: 0.8680 (tt) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.0494 time to fit residues: 5.6140 Evaluate side-chains 80 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.0050 chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 7 optimal weight: 0.0040 chunk 38 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 8 optimal weight: 0.3980 chunk 9 optimal weight: 0.0980 overall best weight: 0.2206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.075601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.062487 restraints weight = 8530.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.064543 restraints weight = 4902.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.065965 restraints weight = 3344.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.066989 restraints weight = 2557.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.067749 restraints weight = 2098.235| |-----------------------------------------------------------------------------| r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3392 Z= 0.113 Angle : 0.665 8.664 4625 Z= 0.332 Chirality : 0.047 0.249 500 Planarity : 0.004 0.034 594 Dihedral : 4.496 21.429 464 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.19 (0.40), residues: 415 helix: -2.28 (0.93), residues: 27 sheet: -0.13 (0.49), residues: 132 loop : -0.97 (0.36), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 466 TYR 0.019 0.001 TYR B 53 PHE 0.015 0.001 PHE B 78 TRP 0.016 0.002 TRP B 112 HIS 0.000 0.000 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.11 ( 3385) covalent geometry : angle 0.66111 / 0.33 ( 4610) SS BOND : bond 0.00691 / 0.33 ( 6) SS BOND : angle 1.57607 / 0.78 ( 12) hydrogen bonds : bond 0.02944 / 1.86 ( 106) hydrogen bonds : angle 6.05143 / 4.11 ( 255) link_NAG-ASN : bond 0.00157 / 0.08 ( 1) link_NAG-ASN : angle 0.95323 / 0.54 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.077 Fit side-chains REVERT: A 452 LEU cc_start: 0.9366 (mt) cc_final: 0.9097 (mt) REVERT: A 467 ASP cc_start: 0.8384 (t70) cc_final: 0.7836 (p0) REVERT: B 120 VAL cc_start: 0.7527 (p) cc_final: 0.7252 (p) REVERT: C 24 GLN cc_start: 0.8415 (tm-30) cc_final: 0.8168 (tm-30) REVERT: C 36 TYR cc_start: 0.8781 (m-10) cc_final: 0.8091 (m-80) REVERT: C 78 LEU cc_start: 0.8919 (tt) cc_final: 0.8682 (tt) REVERT: C 79 GLN cc_start: 0.8771 (mm-40) cc_final: 0.8546 (mm-40) REVERT: C 88 CYS cc_start: 0.5432 (p) cc_final: 0.4924 (p) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.0605 time to fit residues: 6.8639 Evaluate side-chains 78 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 30 optimal weight: 0.1980 chunk 10 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 13 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.074351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.060686 restraints weight = 8676.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.062788 restraints weight = 4897.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.064193 restraints weight = 3329.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.065140 restraints weight = 2545.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.065916 restraints weight = 2122.572| |-----------------------------------------------------------------------------| r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3392 Z= 0.146 Angle : 0.657 8.152 4625 Z= 0.333 Chirality : 0.048 0.250 500 Planarity : 0.004 0.035 594 Dihedral : 4.520 22.892 464 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.16 (0.41), residues: 415 helix: -2.36 (0.91), residues: 27 sheet: -0.10 (0.49), residues: 132 loop : -0.94 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 97 TYR 0.020 0.001 TYR B 53 PHE 0.013 0.001 PHE B 78 TRP 0.012 0.002 TRP B 112 HIS 0.001 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 3385) covalent geometry : angle 0.65249 / 0.33 ( 4610) SS BOND : bond 0.00696 / 0.34 ( 6) SS BOND : angle 1.64446 / 0.86 ( 12) hydrogen bonds : bond 0.03056 / 1.92 ( 106) hydrogen bonds : angle 6.01861 / 4.09 ( 255) link_NAG-ASN : bond 0.00071 / 0.04 ( 1) link_NAG-ASN : angle 1.10878 / 0.63 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 858.63 seconds wall clock time: 15 minutes 28.93 seconds (928.93 seconds total)