Starting phenix.real_space_refine on Wed Jul 1 22:14:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wry_32737/07_2026/7wry_32737.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wry_32737/07_2026/7wry_32737.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7wry_32737/07_2026/7wry_32737.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wry_32737/07_2026/7wry_32737.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wry_32737/07_2026/7wry_32737.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wry_32737/07_2026/7wry_32737.map" model { file = "/net/cci-nas-00/data/ceres_data/7wry_32737/07_2026/7wry_32737.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wry_32737/07_2026/7wry_32737.cif" } resolution = 3.28 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= 0.055 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 2078 2.51 5 N 549 2.21 5 O 626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 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: 3267 Number of models: 1 Model: "" Number of chains: 4 Chain: "R" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1496 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 9, 'TRANS': 178} Chain breaks: 1 Chain: "L" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 802 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Chain: "H" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 930 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 0.89, per 1000 atoms: 0.27 Number of scatterers: 3267 At special positions: 0 Unit cell: (76.68, 81, 73.44, 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 626 8.00 N 549 7.00 C 2078 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, 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=2.06 Simple disulfide: pdb=" SG CYS R 391 " - pdb=" SG CYS R 525 " distance=2.03 Simple disulfide: pdb=" SG CYS R 480 " - pdb=" SG CYS R 488 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 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 A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " NAG-ASN " NAG A 1 " - " ASN R 343 " Time building additional restraints: 0.29 Conformation dependent library (CDL) restraints added in 118.4 milliseconds 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 754 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 9 sheets defined 10.7% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'R' and resid 337 through 341 removed outlier: 3.706A pdb=" N GLU R 340 " --> pdb=" O PRO R 337 " (cutoff:3.500A) Processing helix chain 'R' and resid 365 through 370 Processing helix chain 'R' and resid 383 through 387 Processing helix chain 'R' and resid 405 through 410 removed outlier: 5.153A pdb=" N ARG R 408 " --> pdb=" O ASP R 405 " (cutoff:3.500A) Processing helix chain 'R' and resid 417 through 422 removed outlier: 3.787A pdb=" N TYR R 421 " --> pdb=" O LYS R 417 " (cutoff:3.500A) Processing helix chain 'R' and resid 438 through 443 removed outlier: 3.910A pdb=" N SER R 443 " --> pdb=" O ASN R 439 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.677A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.541A pdb=" N ASP H 90 " --> pdb=" O LYS H 87 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR H 91 " --> pdb=" O ILE H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing sheet with id=AA1, first strand: chain 'R' and resid 356 through 358 removed outlier: 3.636A pdb=" N GLY R 431 " --> pdb=" O TYR R 380 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR R 380 " --> pdb=" O GLY R 431 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 361 through 362 removed outlier: 6.702A pdb=" N CYS R 361 " --> pdb=" O CYS R 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.540A pdb=" N SER L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.273A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.685A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.628A pdb=" N VAL H 18 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.948A pdb=" N ALA H 10 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.948A pdb=" N ALA H 10 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE H 109 " --> pdb=" O ARG H 98 " (cutoff:3.500A) 85 hydrogen bonds defined for protein. 201 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: 0.43 Time building geometry restraints manager: 0.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 1042 1.36 - 1.49: 972 1.49 - 1.62: 1320 1.62 - 1.75: 0 1.75 - 1.88: 16 Bond restraints: 3350 Sorted by residual: bond pdb=" C LYS R 478 " pdb=" N PRO R 479 " ideal model delta sigma weight residual 1.332 1.360 -0.029 1.26e-02 6.30e+03 5.21e+00 bond pdb=" CB CYS R 379 " pdb=" SG CYS R 379 " ideal model delta sigma weight residual 1.808 1.882 -0.074 3.30e-02 9.18e+02 5.05e+00 bond pdb=" N ASN R 487 " pdb=" CA ASN R 487 " ideal model delta sigma weight residual 1.462 1.486 -0.025 1.48e-02 4.57e+03 2.81e+00 bond pdb=" C1 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.08e+00 bond pdb=" C1 BMA A 3 " pdb=" C2 BMA A 3 " ideal model delta sigma weight residual 1.519 1.548 -0.029 2.00e-02 2.50e+03 2.08e+00 ... (remaining 3345 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 4464 2.78 - 5.55: 79 5.55 - 8.33: 9 8.33 - 11.11: 3 11.11 - 13.88: 1 Bond angle restraints: 4556 Sorted by residual: angle pdb=" C TYR R 473 " pdb=" N GLN R 474 " pdb=" CA GLN R 474 " ideal model delta sigma weight residual 120.82 130.37 -9.55 1.50e+00 4.44e-01 4.05e+01 angle pdb=" CA CYS R 432 " pdb=" CB CYS R 432 " pdb=" SG CYS R 432 " ideal model delta sigma weight residual 114.40 128.28 -13.88 2.30e+00 1.89e-01 3.64e+01 angle pdb=" C PHE R 486 " pdb=" N ASN R 487 " pdb=" CA ASN R 487 " ideal model delta sigma weight residual 122.61 131.45 -8.84 1.56e+00 4.11e-01 3.21e+01 angle pdb=" N GLY L 50 " pdb=" CA GLY L 50 " pdb=" C GLY L 50 " ideal model delta sigma weight residual 111.14 103.18 7.96 1.46e+00 4.69e-01 2.97e+01 angle pdb=" N GLN R 474 " pdb=" CA GLN R 474 " pdb=" C GLN R 474 " ideal model delta sigma weight residual 111.37 118.99 -7.62 1.65e+00 3.67e-01 2.13e+01 ... (remaining 4551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.10: 1739 17.10 - 34.19: 150 34.19 - 51.29: 37 51.29 - 68.39: 4 68.39 - 85.48: 7 Dihedral angle restraints: 1937 sinusoidal: 747 harmonic: 1190 Sorted by residual: dihedral pdb=" CA TYR R 473 " pdb=" C TYR R 473 " pdb=" N GLN R 474 " pdb=" CA GLN R 474 " ideal model delta harmonic sigma weight residual 180.00 -143.17 -36.83 0 5.00e+00 4.00e-02 5.43e+01 dihedral pdb=" CB CYS R 379 " pdb=" SG CYS R 379 " pdb=" SG CYS R 432 " pdb=" CB CYS R 432 " ideal model delta sinusoidal sigma weight residual 93.00 44.29 48.71 1 1.00e+01 1.00e-02 3.26e+01 dihedral pdb=" CA GLY L 50 " pdb=" C GLY L 50 " pdb=" N VAL L 51 " pdb=" CA VAL L 51 " ideal model delta harmonic sigma weight residual 180.00 -157.69 -22.31 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 1934 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 394 0.058 - 0.115: 82 0.115 - 0.172: 16 0.172 - 0.229: 4 0.229 - 0.287: 3 Chirality restraints: 499 Sorted by residual: chirality pdb=" C5 BMA A 3 " pdb=" C4 BMA A 3 " pdb=" C6 BMA A 3 " pdb=" O5 BMA A 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CA ASN R 487 " pdb=" N ASN R 487 " pdb=" C ASN R 487 " pdb=" CB ASN R 487 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA GLN R 474 " pdb=" N GLN R 474 " pdb=" C GLN R 474 " pdb=" CB GLN R 474 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 496 not shown) Planarity restraints: 585 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL L 58 " 0.044 5.00e-02 4.00e+02 6.76e-02 7.32e+00 pdb=" N PRO L 59 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO L 59 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO L 59 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER L 14 " 0.038 5.00e-02 4.00e+02 5.72e-02 5.23e+00 pdb=" N PRO L 15 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO L 15 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO L 15 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 486 " 0.009 2.00e-02 2.50e+03 1.91e-02 3.65e+00 pdb=" C PHE R 486 " -0.033 2.00e-02 2.50e+03 pdb=" O PHE R 486 " 0.013 2.00e-02 2.50e+03 pdb=" N ASN R 487 " 0.011 2.00e-02 2.50e+03 ... (remaining 582 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1026 2.83 - 3.35: 2557 3.35 - 3.87: 5385 3.87 - 4.38: 6325 4.38 - 4.90: 10971 Nonbonded interactions: 26264 Sorted by model distance: nonbonded pdb=" OD1 ASP R 442 " pdb=" OH TYR H 103 " model vdw 2.313 3.040 nonbonded pdb=" O ASN R 439 " pdb=" OG SER R 443 " model vdw 2.323 3.040 nonbonded pdb=" OG SER L 63 " pdb=" OG1 THR L 74 " model vdw 2.333 3.040 nonbonded pdb=" OG SER L 65 " pdb=" OG1 THR L 72 " model vdw 2.342 3.040 nonbonded pdb=" OE1 GLU R 406 " pdb=" OH TYR R 495 " model vdw 2.356 3.040 ... (remaining 26259 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 individual isotropic 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: 3.160 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: 0.000 Set scattering table: 0.010 Process input model: 4.830 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 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 0.074 3359 Z= 0.258 Angle : 0.929 13.884 4577 Z= 0.516 Chirality : 0.056 0.287 499 Planarity : 0.007 0.068 584 Dihedral : 14.450 85.483 1165 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.29 % Allowed : 0.00 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -2.76 (0.38), residues: 405 helix: -4.91 (0.29), residues: 27 sheet: -1.33 (0.40), residues: 152 loop : -1.77 (0.37), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG R 457 TYR 0.024 0.002 TYR H 27 PHE 0.029 0.002 PHE R 377 TRP 0.011 0.002 TRP H 47 HIS 0.003 0.001 HIS L 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.26 ( 3350) covalent geometry : angle 0.91472 / 0.51 ( 4556) SS BOND : bond 0.01206 / 0.58 ( 6) SS BOND : angle 2.44374 / 2.36 ( 12) hydrogen bonds : bond 0.27476 / 18.17 ( 81) hydrogen bonds : angle 9.91062 / 6.79 ( 201) link_BETA1-4 : bond 0.00480 / 0.24 ( 2) link_BETA1-4 : angle 2.40944 / 1.61 ( 6) link_NAG-ASN : bond 0.00354 / 0.19 ( 1) link_NAG-ASN : angle 3.38041 / 2.49 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 0.118 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 73 average time/residue: 0.0545 time to fit residues: 5.0337 Evaluate side-chains 70 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN L 27 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.120983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.103925 restraints weight = 4606.649| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.96 r_work: 0.3008 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 3359 Z= 0.235 Angle : 0.661 8.460 4577 Z= 0.348 Chirality : 0.046 0.149 499 Planarity : 0.006 0.051 584 Dihedral : 5.252 24.547 456 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.86 % Allowed : 11.78 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -2.38 (0.38), residues: 405 helix: -4.45 (0.50), residues: 27 sheet: -0.98 (0.42), residues: 148 loop : -1.61 (0.37), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 457 TYR 0.021 0.002 TYR H 27 PHE 0.010 0.001 PHE R 456 TRP 0.011 0.002 TRP H 47 HIS 0.003 0.001 HIS L 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.24 ( 3350) covalent geometry : angle 0.64808 / 0.34 ( 4556) SS BOND : bond 0.00769 / 0.38 ( 6) SS BOND : angle 1.79905 / 1.60 ( 12) hydrogen bonds : bond 0.05214 / 3.41 ( 81) hydrogen bonds : angle 6.75946 / 4.67 ( 201) link_BETA1-4 : bond 0.00420 / 0.21 ( 2) link_BETA1-4 : angle 1.88476 / 1.24 ( 6) link_NAG-ASN : bond 0.00156 / 0.08 ( 1) link_NAG-ASN : angle 3.09016 / 2.37 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 68 time to evaluate : 0.123 Fit side-chains REVERT: H 23 LYS cc_start: 0.8562 (tttp) cc_final: 0.8286 (tttp) REVERT: H 82 GLN cc_start: 0.7619 (mm110) cc_final: 0.7262 (mm-40) REVERT: H 104 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8374 (mm-30) outliers start: 3 outliers final: 2 residues processed: 70 average time/residue: 0.0711 time to fit residues: 6.0961 Evaluate side-chains 68 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 66 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain L residue 63 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 20 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 15 optimal weight: 0.3980 chunk 23 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 92 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.124418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.105542 restraints weight = 4638.582| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.18 r_work: 0.3028 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3359 Z= 0.142 Angle : 0.564 6.968 4577 Z= 0.298 Chirality : 0.044 0.146 499 Planarity : 0.005 0.047 584 Dihedral : 4.786 24.088 456 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.44 % Allowed : 14.66 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -2.05 (0.39), residues: 405 helix: -4.27 (0.58), residues: 27 sheet: -0.80 (0.41), residues: 149 loop : -1.35 (0.38), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 457 TYR 0.020 0.001 TYR H 27 PHE 0.011 0.001 PHE R 456 TRP 0.009 0.001 TRP R 436 HIS 0.003 0.001 HIS L 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 3350) covalent geometry : angle 0.55208 / 0.30 ( 4556) SS BOND : bond 0.00687 / 0.34 ( 6) SS BOND : angle 1.48367 / 1.27 ( 12) hydrogen bonds : bond 0.03846 / 2.55 ( 81) hydrogen bonds : angle 6.03959 / 4.25 ( 201) link_BETA1-4 : bond 0.00463 / 0.23 ( 2) link_BETA1-4 : angle 1.52589 / 0.91 ( 6) link_NAG-ASN : bond 0.00065 / 0.03 ( 1) link_NAG-ASN : angle 3.07896 / 2.28 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.120 Fit side-chains REVERT: L 48 ILE cc_start: 0.8606 (OUTLIER) cc_final: 0.8322 (mp) REVERT: H 3 GLN cc_start: 0.7679 (mt0) cc_final: 0.7293 (pt0) REVERT: H 23 LYS cc_start: 0.8523 (tttp) cc_final: 0.8206 (tttp) REVERT: H 82 GLN cc_start: 0.7833 (mm110) cc_final: 0.7470 (mm110) REVERT: H 95 TYR cc_start: 0.8996 (m-80) cc_final: 0.8756 (m-80) REVERT: H 104 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8307 (mm-30) outliers start: 5 outliers final: 2 residues processed: 73 average time/residue: 0.0689 time to fit residues: 6.1665 Evaluate side-chains 69 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain H residue 28 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 0.5980 chunk 38 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 3 optimal weight: 0.0670 chunk 14 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 92 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.122723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.103762 restraints weight = 4704.947| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.19 r_work: 0.3002 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3359 Z= 0.176 Angle : 0.569 7.457 4577 Z= 0.300 Chirality : 0.044 0.143 499 Planarity : 0.004 0.044 584 Dihedral : 4.644 21.343 456 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 2.01 % Allowed : 14.37 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -1.89 (0.40), residues: 405 helix: -4.17 (0.61), residues: 27 sheet: -0.65 (0.42), residues: 149 loop : -1.27 (0.39), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 457 TYR 0.010 0.001 TYR L 91 PHE 0.009 0.001 PHE R 456 TRP 0.009 0.001 TRP R 436 HIS 0.003 0.001 HIS L 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 ( 3350) covalent geometry : angle 0.55731 / 0.30 ( 4556) SS BOND : bond 0.00603 / 0.30 ( 6) SS BOND : angle 1.46510 / 1.30 ( 12) hydrogen bonds : bond 0.03581 / 2.37 ( 81) hydrogen bonds : angle 5.76433 / 4.06 ( 201) link_BETA1-4 : bond 0.00343 / 0.17 ( 2) link_BETA1-4 : angle 1.52238 / 0.94 ( 6) link_NAG-ASN : bond 0.00076 / 0.04 ( 1) link_NAG-ASN : angle 2.97797 / 2.30 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.131 Fit side-chains REVERT: L 48 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8318 (mp) REVERT: H 23 LYS cc_start: 0.8553 (tttp) cc_final: 0.8233 (tttp) REVERT: H 82 GLN cc_start: 0.7923 (mm110) cc_final: 0.7416 (mm-40) REVERT: H 89 GLU cc_start: 0.8864 (pm20) cc_final: 0.8509 (pm20) outliers start: 7 outliers final: 6 residues processed: 70 average time/residue: 0.0659 time to fit residues: 5.6820 Evaluate side-chains 73 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 340 GLU Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 65 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 12 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 27 optimal weight: 0.0980 chunk 13 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3415 r_free = 0.3415 target = 0.123552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.104924 restraints weight = 4632.023| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.15 r_work: 0.3023 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3359 Z= 0.146 Angle : 0.541 7.050 4577 Z= 0.285 Chirality : 0.043 0.148 499 Planarity : 0.004 0.043 584 Dihedral : 4.454 20.803 456 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 2.87 % Allowed : 14.66 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -1.73 (0.40), residues: 405 helix: -4.13 (0.61), residues: 27 sheet: -0.54 (0.43), residues: 149 loop : -1.14 (0.39), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 98 TYR 0.017 0.001 TYR H 27 PHE 0.006 0.001 PHE R 456 TRP 0.009 0.001 TRP R 436 HIS 0.003 0.001 HIS L 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 ( 3350) covalent geometry : angle 0.52909 / 0.28 ( 4556) SS BOND : bond 0.00595 / 0.29 ( 6) SS BOND : angle 1.37137 / 1.20 ( 12) hydrogen bonds : bond 0.03254 / 2.15 ( 81) hydrogen bonds : angle 5.56218 / 3.92 ( 201) link_BETA1-4 : bond 0.00398 / 0.20 ( 2) link_BETA1-4 : angle 1.41714 / 0.85 ( 6) link_NAG-ASN : bond 0.00002 / 0.00 ( 1) link_NAG-ASN : angle 3.02243 / 2.32 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.121 Fit side-chains REVERT: L 48 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.8287 (mp) REVERT: H 23 LYS cc_start: 0.8557 (tttp) cc_final: 0.8223 (tttp) REVERT: H 82 GLN cc_start: 0.7751 (mm110) cc_final: 0.7462 (mm110) REVERT: H 104 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8320 (tp30) outliers start: 10 outliers final: 7 residues processed: 73 average time/residue: 0.0673 time to fit residues: 5.9609 Evaluate side-chains 75 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 340 GLU Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 65 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 15 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 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 = 0.3415 r_free = 0.3415 target = 0.123560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.104469 restraints weight = 4706.523| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.22 r_work: 0.3012 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3359 Z= 0.151 Angle : 0.550 7.049 4577 Z= 0.288 Chirality : 0.044 0.145 499 Planarity : 0.004 0.042 584 Dihedral : 4.400 20.660 456 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.87 % Allowed : 16.09 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -1.68 (0.41), residues: 405 helix: -4.06 (0.63), residues: 27 sheet: -0.48 (0.43), residues: 149 loop : -1.15 (0.40), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 357 TYR 0.007 0.001 TYR L 91 PHE 0.005 0.001 PHE R 456 TRP 0.009 0.001 TRP R 436 HIS 0.003 0.001 HIS L 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 3350) covalent geometry : angle 0.53870 / 0.29 ( 4556) SS BOND : bond 0.00550 / 0.27 ( 6) SS BOND : angle 1.41879 / 1.23 ( 12) hydrogen bonds : bond 0.03199 / 2.10 ( 81) hydrogen bonds : angle 5.47240 / 3.86 ( 201) link_BETA1-4 : bond 0.00358 / 0.18 ( 2) link_BETA1-4 : angle 1.40923 / 0.85 ( 6) link_NAG-ASN : bond 0.00100 / 0.05 ( 1) link_NAG-ASN : angle 3.04374 / 2.35 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.124 Fit side-chains REVERT: L 48 ILE cc_start: 0.8637 (OUTLIER) cc_final: 0.8364 (mp) REVERT: H 23 LYS cc_start: 0.8574 (tttp) cc_final: 0.8235 (tttp) REVERT: H 82 GLN cc_start: 0.7727 (mm110) cc_final: 0.7494 (mm110) REVERT: H 104 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8385 (mm-30) outliers start: 10 outliers final: 8 residues processed: 72 average time/residue: 0.0655 time to fit residues: 5.8321 Evaluate side-chains 75 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 340 GLU Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 65 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 92 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.123696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.104620 restraints weight = 4732.486| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.22 r_work: 0.3015 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3359 Z= 0.151 Angle : 0.546 6.818 4577 Z= 0.286 Chirality : 0.044 0.147 499 Planarity : 0.004 0.041 584 Dihedral : 4.380 20.950 456 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.87 % Allowed : 15.80 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -1.62 (0.41), residues: 405 helix: -4.05 (0.63), residues: 27 sheet: -0.45 (0.43), residues: 149 loop : -1.09 (0.40), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 457 TYR 0.017 0.001 TYR H 27 PHE 0.005 0.001 PHE R 456 TRP 0.009 0.001 TRP R 436 HIS 0.003 0.001 HIS L 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 3350) covalent geometry : angle 0.53401 / 0.28 ( 4556) SS BOND : bond 0.00598 / 0.29 ( 6) SS BOND : angle 1.53753 / 1.36 ( 12) hydrogen bonds : bond 0.03100 / 2.03 ( 81) hydrogen bonds : angle 5.37688 / 3.79 ( 201) link_BETA1-4 : bond 0.00365 / 0.18 ( 2) link_BETA1-4 : angle 1.37698 / 0.82 ( 6) link_NAG-ASN : bond 0.00091 / 0.05 ( 1) link_NAG-ASN : angle 3.01808 / 2.34 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.070 Fit side-chains REVERT: L 48 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8377 (mp) REVERT: H 23 LYS cc_start: 0.8503 (tttp) cc_final: 0.8186 (tttp) REVERT: H 82 GLN cc_start: 0.7736 (mm110) cc_final: 0.7500 (mm110) REVERT: H 104 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8437 (mm-30) outliers start: 10 outliers final: 8 residues processed: 70 average time/residue: 0.0509 time to fit residues: 4.3337 Evaluate side-chains 74 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 340 GLU Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 65 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 23 optimal weight: 0.0770 chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 = 0.3419 r_free = 0.3419 target = 0.123823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.104873 restraints weight = 4814.953| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.22 r_work: 0.3015 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3359 Z= 0.144 Angle : 0.542 6.567 4577 Z= 0.284 Chirality : 0.043 0.147 499 Planarity : 0.004 0.041 584 Dihedral : 4.353 19.723 456 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.59 % Allowed : 17.53 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -1.60 (0.41), residues: 405 helix: -4.05 (0.63), residues: 27 sheet: -0.42 (0.44), residues: 149 loop : -1.09 (0.40), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 98 TYR 0.008 0.001 TYR H 103 PHE 0.004 0.001 PHE R 456 TRP 0.009 0.001 TRP R 436 HIS 0.003 0.001 HIS L 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 ( 3350) covalent geometry : angle 0.52914 / 0.28 ( 4556) SS BOND : bond 0.00562 / 0.27 ( 6) SS BOND : angle 1.51845 / 1.32 ( 12) hydrogen bonds : bond 0.02993 / 1.95 ( 81) hydrogen bonds : angle 5.30932 / 3.75 ( 201) link_BETA1-4 : bond 0.00419 / 0.21 ( 2) link_BETA1-4 : angle 1.36717 / 0.81 ( 6) link_NAG-ASN : bond 0.00088 / 0.05 ( 1) link_NAG-ASN : angle 3.04836 / 2.35 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.073 Fit side-chains REVERT: L 48 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8379 (mp) REVERT: H 23 LYS cc_start: 0.8491 (tttp) cc_final: 0.8171 (tttp) REVERT: H 82 GLN cc_start: 0.7733 (mm110) cc_final: 0.7494 (mm110) REVERT: H 104 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8456 (mm-30) outliers start: 9 outliers final: 8 residues processed: 73 average time/residue: 0.0517 time to fit residues: 4.7033 Evaluate side-chains 76 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 340 GLU Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 65 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 35 optimal weight: 0.6980 chunk 29 optimal weight: 0.2980 chunk 5 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 14 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3421 r_free = 0.3421 target = 0.123811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.104940 restraints weight = 4732.702| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.19 r_work: 0.3019 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3359 Z= 0.148 Angle : 0.548 6.549 4577 Z= 0.287 Chirality : 0.044 0.146 499 Planarity : 0.004 0.041 584 Dihedral : 4.340 20.249 456 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.87 % Allowed : 17.53 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -1.51 (0.41), residues: 405 helix: -4.04 (0.63), residues: 27 sheet: -0.37 (0.44), residues: 148 loop : -1.00 (0.40), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 98 TYR 0.019 0.001 TYR H 27 PHE 0.004 0.001 PHE R 456 TRP 0.008 0.001 TRP R 436 HIS 0.003 0.001 HIS L 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 3350) covalent geometry : angle 0.53617 / 0.28 ( 4556) SS BOND : bond 0.00561 / 0.27 ( 6) SS BOND : angle 1.50674 / 1.31 ( 12) hydrogen bonds : bond 0.02979 / 1.92 ( 81) hydrogen bonds : angle 5.28285 / 3.72 ( 201) link_BETA1-4 : bond 0.00356 / 0.18 ( 2) link_BETA1-4 : angle 1.34648 / 0.80 ( 6) link_NAG-ASN : bond 0.00142 / 0.07 ( 1) link_NAG-ASN : angle 3.02585 / 2.34 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.138 Fit side-chains REVERT: L 48 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8396 (mp) REVERT: H 23 LYS cc_start: 0.8475 (tttp) cc_final: 0.8147 (tttp) REVERT: H 82 GLN cc_start: 0.7726 (mm110) cc_final: 0.7486 (mm110) REVERT: H 104 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8451 (mm-30) outliers start: 10 outliers final: 9 residues processed: 71 average time/residue: 0.0725 time to fit residues: 6.3739 Evaluate side-chains 78 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 340 GLU Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 2 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.122247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.103406 restraints weight = 4752.757| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.19 r_work: 0.3005 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3359 Z= 0.181 Angle : 0.567 7.059 4577 Z= 0.297 Chirality : 0.044 0.145 499 Planarity : 0.004 0.040 584 Dihedral : 4.447 19.781 456 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.87 % Allowed : 17.53 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -1.51 (0.41), residues: 405 helix: -4.02 (0.64), residues: 27 sheet: -0.35 (0.44), residues: 147 loop : -1.02 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 98 TYR 0.010 0.001 TYR H 103 PHE 0.004 0.001 PHE R 456 TRP 0.008 0.001 TRP H 50 HIS 0.003 0.001 HIS L 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 ( 3350) covalent geometry : angle 0.55462 / 0.29 ( 4556) SS BOND : bond 0.00574 / 0.28 ( 6) SS BOND : angle 1.63336 / 1.43 ( 12) hydrogen bonds : bond 0.03145 / 2.02 ( 81) hydrogen bonds : angle 5.33859 / 3.77 ( 201) link_BETA1-4 : bond 0.00342 / 0.17 ( 2) link_BETA1-4 : angle 1.39655 / 0.84 ( 6) link_NAG-ASN : bond 0.00234 / 0.12 ( 1) link_NAG-ASN : angle 2.94407 / 2.32 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.120 Fit side-chains REVERT: L 36 TYR cc_start: 0.9273 (m-80) cc_final: 0.9014 (m-80) REVERT: L 48 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8368 (mp) REVERT: H 23 LYS cc_start: 0.8486 (tttp) cc_final: 0.8144 (tttp) REVERT: H 82 GLN cc_start: 0.7724 (mm110) cc_final: 0.7486 (mm110) REVERT: H 104 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8390 (mm-30) outliers start: 10 outliers final: 9 residues processed: 71 average time/residue: 0.0536 time to fit residues: 4.6963 Evaluate side-chains 77 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 340 GLU Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3412 r_free = 0.3412 target = 0.122960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.104089 restraints weight = 4799.590| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.20 r_work: 0.3010 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3359 Z= 0.160 Angle : 0.549 6.830 4577 Z= 0.287 Chirality : 0.044 0.146 499 Planarity : 0.004 0.040 584 Dihedral : 4.395 20.663 456 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.87 % Allowed : 17.53 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -1.50 (0.42), residues: 405 helix: -4.03 (0.63), residues: 27 sheet: -0.38 (0.44), residues: 148 loop : -0.99 (0.41), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 98 TYR 0.018 0.001 TYR H 27 PHE 0.004 0.001 PHE R 456 TRP 0.008 0.001 TRP H 47 HIS 0.003 0.001 HIS L 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 ( 3350) covalent geometry : angle 0.53725 / 0.28 ( 4556) SS BOND : bond 0.00566 / 0.28 ( 6) SS BOND : angle 1.55882 / 1.36 ( 12) hydrogen bonds : bond 0.03026 / 1.94 ( 81) hydrogen bonds : angle 5.29689 / 3.73 ( 201) link_BETA1-4 : bond 0.00341 / 0.17 ( 2) link_BETA1-4 : angle 1.34555 / 0.79 ( 6) link_NAG-ASN : bond 0.00138 / 0.07 ( 1) link_NAG-ASN : angle 2.97341 / 2.32 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1060.85 seconds wall clock time: 18 minutes 52.96 seconds (1132.96 seconds total)