Starting phenix.real_space_refine on Wed Jul 1 21:10:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8di5_27439/07_2026/8di5_27439.cif Found real_map, /net/cci-nas-00/data/ceres_data/8di5_27439/07_2026/8di5_27439.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8di5_27439/07_2026/8di5_27439.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8di5_27439/07_2026/8di5_27439.map" model { file = "/net/cci-nas-00/data/ceres_data/8di5_27439/07_2026/8di5_27439.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8di5_27439/07_2026/8di5_27439.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8di5_27439/07_2026/8di5_27439.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8di5_27439/07_2026/8di5_27439.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 1573 2.51 5 N 409 2.21 5 O 473 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 2467 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1546 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "H" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 907 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "C" 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: 0.80, per 1000 atoms: 0.32 Number of scatterers: 2467 At special positions: 0 Unit cell: (68, 79, 73, 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 12 16.00 O 473 8.00 N 409 7.00 C 1573 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " 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 NAG-ASN " NAG C1301 " - " ASN C 343 " Time building additional restraints: 0.11 Conformation dependent library (CDL) restraints added in 65.3 milliseconds 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 568 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 5 sheets defined 15.8% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.645A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 5.008A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'H' and resid 53 through 55 No H-bonds generated for 'chain 'H' and resid 53 through 55' Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.962A pdb=" N LYS H 64 " --> pdb=" O PRO H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 86 through 90 removed outlier: 4.065A pdb=" N THR H 90 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 354 through 358 removed outlier: 5.268A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'H' and resid 6 through 7 Processing sheet with id=AA4, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.296A pdb=" N GLU H 33 " --> pdb=" O VAL H 98 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N MET H 34 " --> pdb=" O ASN H 50 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASN H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 80 hydrogen bonds defined for protein. 204 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: 0.39 Time building geometry restraints manager: 0.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 786 1.34 - 1.46: 698 1.46 - 1.58: 1036 1.58 - 1.70: 0 1.70 - 1.82: 14 Bond restraints: 2534 Sorted by residual: bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.50e+00 bond pdb=" CB TRP H 47 " pdb=" CG TRP H 47 " ideal model delta sigma weight residual 1.498 1.450 0.048 3.10e-02 1.04e+03 2.39e+00 bond pdb=" CB ILE C 472 " pdb=" CG2 ILE C 472 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.22e+00 bond pdb=" CB ASN H 83 " pdb=" CG ASN H 83 " ideal model delta sigma weight residual 1.516 1.549 -0.033 2.50e-02 1.60e+03 1.75e+00 bond pdb=" CG LEU C 452 " pdb=" CD1 LEU C 452 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.67e+00 ... (remaining 2529 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.77: 3417 3.77 - 7.54: 26 7.54 - 11.31: 3 11.31 - 15.08: 0 15.08 - 18.85: 1 Bond angle restraints: 3447 Sorted by residual: angle pdb=" CA LEU C 518 " pdb=" CB LEU C 518 " pdb=" CG LEU C 518 " ideal model delta sigma weight residual 116.30 135.15 -18.85 3.50e+00 8.16e-02 2.90e+01 angle pdb=" C GLU H 33 " pdb=" N MET H 34 " pdb=" CA MET H 34 " ideal model delta sigma weight residual 122.87 118.15 4.72 1.61e+00 3.86e-01 8.60e+00 angle pdb=" C LEU C 517 " pdb=" N LEU C 518 " pdb=" CA LEU C 518 " ideal model delta sigma weight residual 122.68 126.77 -4.09 1.47e+00 4.63e-01 7.72e+00 angle pdb=" CA TYR C 495 " pdb=" CB TYR C 495 " pdb=" CG TYR C 495 " ideal model delta sigma weight residual 113.90 118.77 -4.87 1.80e+00 3.09e-01 7.31e+00 angle pdb=" CA TYR C 473 " pdb=" CB TYR C 473 " pdb=" CG TYR C 473 " ideal model delta sigma weight residual 113.90 118.55 -4.65 1.80e+00 3.09e-01 6.69e+00 ... (remaining 3442 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.12: 1315 15.12 - 30.23: 128 30.23 - 45.35: 21 45.35 - 60.47: 3 60.47 - 75.58: 2 Dihedral angle restraints: 1469 sinusoidal: 568 harmonic: 901 Sorted by residual: dihedral pdb=" CA ALA C 520 " pdb=" C ALA C 520 " pdb=" N PRO C 521 " pdb=" CA PRO C 521 " ideal model delta harmonic sigma weight residual 180.00 159.25 20.75 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA LEU C 517 " pdb=" C LEU C 517 " pdb=" N LEU C 518 " pdb=" CA LEU C 518 " ideal model delta harmonic sigma weight residual 180.00 159.50 20.50 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 95 " pdb=" CB CYS H 95 " ideal model delta sinusoidal sigma weight residual 93.00 62.46 30.54 1 1.00e+01 1.00e-02 1.33e+01 ... (remaining 1466 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 207 0.038 - 0.077: 95 0.077 - 0.115: 37 0.115 - 0.154: 22 0.154 - 0.192: 3 Chirality restraints: 364 Sorted by residual: chirality pdb=" CA ILE C 434 " pdb=" N ILE C 434 " pdb=" C ILE C 434 " pdb=" CB ILE C 434 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.22e-01 chirality pdb=" CA LEU C 518 " pdb=" N LEU C 518 " pdb=" C LEU C 518 " pdb=" CB LEU C 518 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.91e-01 chirality pdb=" CB THR H 90 " pdb=" CA THR H 90 " pdb=" OG1 THR H 90 " pdb=" CG2 THR H 90 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.76e-01 ... (remaining 361 not shown) Planarity restraints: 448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 520 " -0.038 5.00e-02 4.00e+02 5.69e-02 5.18e+00 pdb=" N PRO C 521 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO C 521 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 521 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 462 " 0.036 5.00e-02 4.00e+02 5.40e-02 4.66e+00 pdb=" N PRO C 463 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 463 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 463 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 362 " -0.009 2.00e-02 2.50e+03 1.90e-02 3.62e+00 pdb=" C VAL C 362 " 0.033 2.00e-02 2.50e+03 pdb=" O VAL C 362 " -0.012 2.00e-02 2.50e+03 pdb=" N ALA C 363 " -0.011 2.00e-02 2.50e+03 ... (remaining 445 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 757 2.82 - 3.34: 1959 3.34 - 3.86: 4099 3.86 - 4.38: 4610 4.38 - 4.90: 8120 Nonbonded interactions: 19545 Sorted by model distance: nonbonded pdb=" OG SER C 359 " pdb=" OD1 ASN C 394 " model vdw 2.300 3.040 nonbonded pdb=" O ASN C 481 " pdb=" NE2 GLN H 39 " model vdw 2.328 3.120 nonbonded pdb=" OD1 ASP C 442 " pdb=" OH TYR C 451 " model vdw 2.364 3.040 nonbonded pdb=" NH2 ARG C 454 " pdb=" O ASP C 467 " model vdw 2.390 3.120 nonbonded pdb=" OG SER H 117 " pdb=" N SER H 118 " model vdw 2.392 3.120 ... (remaining 19540 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.600 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 4.480 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 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 0.049 2540 Z= 0.266 Angle : 0.954 18.847 3460 Z= 0.483 Chirality : 0.057 0.192 364 Planarity : 0.007 0.057 447 Dihedral : 12.370 75.582 886 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.38 % Allowed : 1.51 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.41), residues: 307 helix: -4.35 (0.46), residues: 33 sheet: 0.00 (0.51), residues: 90 loop : -1.97 (0.37), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 355 TYR 0.028 0.003 TYR C 495 PHE 0.032 0.004 PHE C 347 TRP 0.012 0.002 TRP C 436 HIS 0.001 0.000 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00606 / 0.27 ( 2534) covalent geometry : angle 0.95118 / 0.48 ( 3447) SS BOND : bond 0.00324 / 0.18 ( 5) SS BOND : angle 1.25721 / 0.71 ( 10) hydrogen bonds : bond 0.17742 / 10.89 ( 75) hydrogen bonds : angle 9.94340 / 6.63 ( 204) link_NAG-ASN : bond 0.00313 / 0.16 ( 1) link_NAG-ASN : angle 1.96518 / 1.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.063 Fit side-chains revert: symmetry clash REVERT: C 386 LYS cc_start: 0.8480 (mmtp) cc_final: 0.7349 (ttpt) REVERT: H 20 LEU cc_start: 0.8405 (mt) cc_final: 0.8196 (mt) outliers start: 1 outliers final: 0 residues processed: 84 average time/residue: 0.0989 time to fit residues: 9.3464 Evaluate side-chains 67 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 437 ASN C 481 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.111746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.094556 restraints weight = 4313.368| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.91 r_work: 0.3117 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 2540 Z= 0.211 Angle : 0.646 11.538 3460 Z= 0.332 Chirality : 0.044 0.157 364 Planarity : 0.005 0.041 447 Dihedral : 5.269 18.860 348 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.26 % Allowed : 11.32 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.43), residues: 307 helix: -3.49 (0.61), residues: 34 sheet: 0.16 (0.53), residues: 90 loop : -1.73 (0.40), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 355 TYR 0.021 0.001 TYR C 495 PHE 0.015 0.002 PHE H 107 TRP 0.010 0.001 TRP C 436 HIS 0.000 0.000 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.21 ( 2534) covalent geometry : angle 0.64452 / 0.33 ( 3447) SS BOND : bond 0.00190 / 0.12 ( 5) SS BOND : angle 0.70309 / 0.40 ( 10) hydrogen bonds : bond 0.03969 / 2.38 ( 75) hydrogen bonds : angle 7.39149 / 4.96 ( 204) link_NAG-ASN : bond 0.00442 / 0.23 ( 1) link_NAG-ASN : angle 1.54229 / 0.79 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.100 Fit side-chains REVERT: C 356 LYS cc_start: 0.8543 (tptm) cc_final: 0.8289 (tptm) REVERT: C 378 LYS cc_start: 0.8780 (mttm) cc_final: 0.8564 (mtpt) REVERT: C 386 LYS cc_start: 0.8505 (mmtp) cc_final: 0.7395 (ttpt) REVERT: C 403 ARG cc_start: 0.8725 (ptt180) cc_final: 0.8306 (ptt180) REVERT: H 22 CYS cc_start: 0.7186 (t) cc_final: 0.6947 (t) outliers start: 6 outliers final: 3 residues processed: 81 average time/residue: 0.0926 time to fit residues: 8.4459 Evaluate side-chains 74 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain H residue 112 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 19 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 17 optimal weight: 0.4980 chunk 23 optimal weight: 0.1980 chunk 6 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 481 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.112475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.094750 restraints weight = 4405.780| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 3.07 r_work: 0.3126 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2540 Z= 0.144 Angle : 0.578 10.019 3460 Z= 0.297 Chirality : 0.043 0.145 364 Planarity : 0.004 0.034 447 Dihedral : 4.921 18.201 348 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.26 % Allowed : 13.96 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.44), residues: 307 helix: -3.08 (0.77), residues: 34 sheet: 0.35 (0.53), residues: 90 loop : -1.56 (0.41), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 66 TYR 0.018 0.001 TYR C 495 PHE 0.010 0.001 PHE C 347 TRP 0.009 0.001 TRP C 436 HIS 0.000 0.000 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 2534) covalent geometry : angle 0.57766 / 0.30 ( 3447) SS BOND : bond 0.00141 / 0.09 ( 5) SS BOND : angle 0.42489 / 0.24 ( 10) hydrogen bonds : bond 0.03424 / 2.08 ( 75) hydrogen bonds : angle 6.85954 / 4.61 ( 204) link_NAG-ASN : bond 0.00326 / 0.17 ( 1) link_NAG-ASN : angle 1.34184 / 0.71 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.096 Fit side-chains REVERT: C 378 LYS cc_start: 0.8784 (mttm) cc_final: 0.8526 (mtpt) REVERT: C 386 LYS cc_start: 0.8448 (mmtp) cc_final: 0.7286 (ttpt) REVERT: C 501 TYR cc_start: 0.8802 (OUTLIER) cc_final: 0.8477 (m-10) REVERT: H 22 CYS cc_start: 0.7242 (t) cc_final: 0.6981 (t) outliers start: 6 outliers final: 3 residues processed: 77 average time/residue: 0.0913 time to fit residues: 7.9181 Evaluate side-chains 75 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain H residue 112 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 17 optimal weight: 0.3980 chunk 8 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 0 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 481 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.111325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.093648 restraints weight = 4349.274| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 3.05 r_work: 0.3118 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2540 Z= 0.154 Angle : 0.571 8.482 3460 Z= 0.292 Chirality : 0.044 0.142 364 Planarity : 0.004 0.035 447 Dihedral : 4.784 17.891 348 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.64 % Allowed : 14.72 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.46), residues: 307 helix: -2.98 (0.82), residues: 34 sheet: 0.78 (0.56), residues: 82 loop : -1.48 (0.42), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 408 TYR 0.018 0.001 TYR C 495 PHE 0.009 0.001 PHE C 347 TRP 0.008 0.001 TRP C 436 HIS 0.000 0.000 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 2534) covalent geometry : angle 0.57026 / 0.29 ( 3447) SS BOND : bond 0.00146 / 0.09 ( 5) SS BOND : angle 0.41141 / 0.23 ( 10) hydrogen bonds : bond 0.03305 / 1.97 ( 75) hydrogen bonds : angle 6.55716 / 4.41 ( 204) link_NAG-ASN : bond 0.00322 / 0.17 ( 1) link_NAG-ASN : angle 1.22092 / 0.64 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.094 Fit side-chains REVERT: C 378 LYS cc_start: 0.8779 (mttm) cc_final: 0.8526 (mtpp) REVERT: C 386 LYS cc_start: 0.8462 (mmtp) cc_final: 0.7313 (ttpt) REVERT: C 501 TYR cc_start: 0.8840 (OUTLIER) cc_final: 0.8549 (m-10) REVERT: H 22 CYS cc_start: 0.7277 (t) cc_final: 0.7036 (t) REVERT: H 72 ASP cc_start: 0.8464 (t0) cc_final: 0.8046 (t0) REVERT: H 79 TYR cc_start: 0.7969 (m-10) cc_final: 0.7581 (m-10) outliers start: 7 outliers final: 4 residues processed: 80 average time/residue: 0.0860 time to fit residues: 7.7254 Evaluate side-chains 75 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 112 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 19 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 481 ASN C 506 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.110387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.092933 restraints weight = 4380.690| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 3.02 r_work: 0.3103 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2540 Z= 0.183 Angle : 0.578 8.363 3460 Z= 0.298 Chirality : 0.044 0.141 364 Planarity : 0.004 0.034 447 Dihedral : 4.839 18.583 348 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.64 % Allowed : 15.47 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.46), residues: 307 helix: -3.09 (0.79), residues: 34 sheet: 0.67 (0.54), residues: 88 loop : -1.42 (0.44), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 355 TYR 0.019 0.001 TYR C 495 PHE 0.011 0.002 PHE C 456 TRP 0.009 0.001 TRP C 436 HIS 0.000 0.000 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 ( 2534) covalent geometry : angle 0.57779 / 0.30 ( 3447) SS BOND : bond 0.00229 / 0.14 ( 5) SS BOND : angle 0.48417 / 0.26 ( 10) hydrogen bonds : bond 0.03345 / 2.01 ( 75) hydrogen bonds : angle 6.48068 / 4.36 ( 204) link_NAG-ASN : bond 0.00322 / 0.17 ( 1) link_NAG-ASN : angle 1.21876 / 0.64 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.102 Fit side-chains REVERT: C 378 LYS cc_start: 0.8802 (mttm) cc_final: 0.8536 (mtpt) REVERT: C 386 LYS cc_start: 0.8530 (mmtp) cc_final: 0.7465 (ttpt) REVERT: C 403 ARG cc_start: 0.8686 (ptt180) cc_final: 0.8458 (ptt180) REVERT: H 19 ARG cc_start: 0.8394 (ttm110) cc_final: 0.7695 (ttm110) REVERT: H 22 CYS cc_start: 0.7255 (t) cc_final: 0.7017 (t) REVERT: H 72 ASP cc_start: 0.8442 (t0) cc_final: 0.8008 (t0) REVERT: H 79 TYR cc_start: 0.7982 (m-10) cc_final: 0.7594 (m-10) REVERT: H 81 GLN cc_start: 0.7458 (tm-30) cc_final: 0.7212 (tt0) outliers start: 7 outliers final: 3 residues processed: 80 average time/residue: 0.0969 time to fit residues: 8.7060 Evaluate side-chains 75 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 112 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.0870 chunk 14 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 9 optimal weight: 0.2980 chunk 10 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 481 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.111128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.093541 restraints weight = 4339.703| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 3.00 r_work: 0.3115 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2540 Z= 0.159 Angle : 0.562 7.890 3460 Z= 0.291 Chirality : 0.044 0.163 364 Planarity : 0.004 0.035 447 Dihedral : 4.795 17.949 348 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.26 % Allowed : 16.98 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.46), residues: 307 helix: -3.19 (0.75), residues: 34 sheet: 0.77 (0.55), residues: 82 loop : -1.30 (0.43), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 66 TYR 0.018 0.001 TYR C 495 PHE 0.008 0.001 PHE C 347 TRP 0.009 0.001 TRP C 436 HIS 0.000 0.000 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 ( 2534) covalent geometry : angle 0.56102 / 0.29 ( 3447) SS BOND : bond 0.00170 / 0.11 ( 5) SS BOND : angle 0.41262 / 0.22 ( 10) hydrogen bonds : bond 0.03248 / 1.98 ( 75) hydrogen bonds : angle 6.39411 / 4.33 ( 204) link_NAG-ASN : bond 0.00301 / 0.16 ( 1) link_NAG-ASN : angle 1.24483 / 0.66 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.121 Fit side-chains REVERT: C 378 LYS cc_start: 0.8812 (mttm) cc_final: 0.8529 (mtpt) REVERT: C 386 LYS cc_start: 0.8521 (mmtp) cc_final: 0.7469 (ttpt) REVERT: C 403 ARG cc_start: 0.8687 (ptt180) cc_final: 0.8461 (ptt180) REVERT: C 405 ASP cc_start: 0.8266 (p0) cc_final: 0.8056 (p0) REVERT: H 22 CYS cc_start: 0.7185 (t) cc_final: 0.6947 (t) REVERT: H 72 ASP cc_start: 0.8438 (t0) cc_final: 0.8007 (t0) REVERT: H 79 TYR cc_start: 0.7972 (m-10) cc_final: 0.7626 (m-10) outliers start: 6 outliers final: 5 residues processed: 80 average time/residue: 0.0937 time to fit residues: 8.4120 Evaluate side-chains 78 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 112 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 0.1980 chunk 7 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 481 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.109967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.092375 restraints weight = 4371.410| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 3.04 r_work: 0.3094 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2540 Z= 0.191 Angle : 0.577 7.766 3460 Z= 0.301 Chirality : 0.044 0.137 364 Planarity : 0.004 0.035 447 Dihedral : 4.873 17.605 348 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.02 % Allowed : 16.98 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.46), residues: 307 helix: -3.16 (0.77), residues: 34 sheet: 0.51 (0.53), residues: 88 loop : -1.29 (0.44), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 66 TYR 0.019 0.002 TYR C 495 PHE 0.012 0.002 PHE C 456 TRP 0.009 0.001 TRP H 47 HIS 0.000 0.000 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 ( 2534) covalent geometry : angle 0.57607 / 0.30 ( 3447) SS BOND : bond 0.00161 / 0.10 ( 5) SS BOND : angle 0.46756 / 0.25 ( 10) hydrogen bonds : bond 0.03336 / 2.02 ( 75) hydrogen bonds : angle 6.41252 / 4.34 ( 204) link_NAG-ASN : bond 0.00291 / 0.15 ( 1) link_NAG-ASN : angle 1.33282 / 0.71 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.091 Fit side-chains REVERT: C 378 LYS cc_start: 0.8793 (mttm) cc_final: 0.8523 (mtpt) REVERT: C 386 LYS cc_start: 0.8544 (mmtp) cc_final: 0.7484 (ttpt) REVERT: C 403 ARG cc_start: 0.8659 (ptt180) cc_final: 0.8410 (ptt180) REVERT: C 405 ASP cc_start: 0.8361 (p0) cc_final: 0.8149 (p0) REVERT: H 22 CYS cc_start: 0.7255 (t) cc_final: 0.7014 (t) REVERT: H 66 ARG cc_start: 0.8631 (mtm110) cc_final: 0.8390 (mtm110) REVERT: H 72 ASP cc_start: 0.8415 (t0) cc_final: 0.7982 (t0) REVERT: H 79 TYR cc_start: 0.7983 (m-10) cc_final: 0.7624 (m-10) outliers start: 8 outliers final: 6 residues processed: 79 average time/residue: 0.1066 time to fit residues: 9.3947 Evaluate side-chains 78 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 112 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 4 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.0770 chunk 0 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 481 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.110986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.093233 restraints weight = 4392.907| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 3.06 r_work: 0.3108 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2540 Z= 0.155 Angle : 0.563 7.567 3460 Z= 0.293 Chirality : 0.043 0.136 364 Planarity : 0.004 0.034 447 Dihedral : 4.800 17.386 348 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.64 % Allowed : 18.49 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.46), residues: 307 helix: -3.07 (0.93), residues: 27 sheet: 0.52 (0.54), residues: 88 loop : -1.33 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 19 TYR 0.017 0.001 TYR C 495 PHE 0.008 0.001 PHE C 347 TRP 0.009 0.001 TRP C 436 HIS 0.000 0.000 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 2534) covalent geometry : angle 0.56239 / 0.29 ( 3447) SS BOND : bond 0.00154 / 0.10 ( 5) SS BOND : angle 0.40708 / 0.21 ( 10) hydrogen bonds : bond 0.03196 / 1.92 ( 75) hydrogen bonds : angle 6.32441 / 4.29 ( 204) link_NAG-ASN : bond 0.00260 / 0.14 ( 1) link_NAG-ASN : angle 1.34099 / 0.72 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.091 Fit side-chains REVERT: C 378 LYS cc_start: 0.8792 (mttm) cc_final: 0.8501 (mtpt) REVERT: C 386 LYS cc_start: 0.8513 (mmtp) cc_final: 0.7489 (ttpt) REVERT: C 403 ARG cc_start: 0.8645 (ptt180) cc_final: 0.8397 (ptt180) REVERT: C 405 ASP cc_start: 0.8375 (p0) cc_final: 0.8169 (p0) REVERT: H 22 CYS cc_start: 0.7222 (t) cc_final: 0.6975 (t) REVERT: H 66 ARG cc_start: 0.8604 (mtm110) cc_final: 0.8297 (mtm110) REVERT: H 72 ASP cc_start: 0.8362 (t0) cc_final: 0.7952 (t0) REVERT: H 79 TYR cc_start: 0.7979 (m-10) cc_final: 0.7621 (m-10) outliers start: 7 outliers final: 6 residues processed: 78 average time/residue: 0.0952 time to fit residues: 8.3197 Evaluate side-chains 81 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 112 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 8 optimal weight: 0.0980 chunk 26 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 17 optimal weight: 0.3980 chunk 9 optimal weight: 0.6980 chunk 11 optimal weight: 0.0060 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 481 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.112504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.094777 restraints weight = 4394.304| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 3.05 r_work: 0.3131 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2540 Z= 0.121 Angle : 0.543 7.481 3460 Z= 0.282 Chirality : 0.043 0.137 364 Planarity : 0.003 0.037 447 Dihedral : 4.599 17.121 348 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.89 % Allowed : 18.87 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.47), residues: 307 helix: -3.03 (0.94), residues: 27 sheet: 0.75 (0.56), residues: 82 loop : -1.28 (0.43), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 19 TYR 0.016 0.001 TYR H 32 PHE 0.012 0.001 PHE C 456 TRP 0.010 0.001 TRP C 436 HIS 0.000 0.000 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 2534) covalent geometry : angle 0.54280 / 0.28 ( 3447) SS BOND : bond 0.00136 / 0.09 ( 5) SS BOND : angle 0.35559 / 0.18 ( 10) hydrogen bonds : bond 0.03022 / 1.80 ( 75) hydrogen bonds : angle 6.18123 / 4.21 ( 204) link_NAG-ASN : bond 0.00253 / 0.13 ( 1) link_NAG-ASN : angle 1.27518 / 0.69 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.060 Fit side-chains REVERT: C 378 LYS cc_start: 0.8791 (mttm) cc_final: 0.8502 (mtpt) REVERT: C 386 LYS cc_start: 0.8451 (mmtp) cc_final: 0.7385 (ttpt) REVERT: C 403 ARG cc_start: 0.8637 (ptt180) cc_final: 0.8387 (ptt180) REVERT: H 19 ARG cc_start: 0.8603 (ttm-80) cc_final: 0.7994 (ttm110) REVERT: H 22 CYS cc_start: 0.7223 (t) cc_final: 0.6969 (t) REVERT: H 66 ARG cc_start: 0.8578 (mtm110) cc_final: 0.8260 (mtm110) REVERT: H 72 ASP cc_start: 0.8349 (t0) cc_final: 0.7945 (t0) REVERT: H 79 TYR cc_start: 0.7970 (m-10) cc_final: 0.7615 (m-10) REVERT: H 113 LEU cc_start: 0.8807 (tt) cc_final: 0.8523 (mp) outliers start: 5 outliers final: 4 residues processed: 76 average time/residue: 0.0953 time to fit residues: 8.0794 Evaluate side-chains 76 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 112 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 10 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 481 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.111391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.093656 restraints weight = 4452.291| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 3.07 r_work: 0.3116 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 2540 Z= 0.173 Angle : 0.575 7.428 3460 Z= 0.297 Chirality : 0.044 0.162 364 Planarity : 0.004 0.037 447 Dihedral : 4.744 17.173 348 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.26 % Allowed : 20.00 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.47), residues: 307 helix: -3.04 (0.94), residues: 27 sheet: 0.68 (0.56), residues: 82 loop : -1.29 (0.43), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 19 TYR 0.018 0.001 TYR C 495 PHE 0.008 0.001 PHE C 347 TRP 0.008 0.001 TRP C 436 HIS 0.000 0.000 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 ( 2534) covalent geometry : angle 0.57460 / 0.30 ( 3447) SS BOND : bond 0.00139 / 0.09 ( 5) SS BOND : angle 0.43283 / 0.23 ( 10) hydrogen bonds : bond 0.03239 / 1.93 ( 75) hydrogen bonds : angle 6.22152 / 4.22 ( 204) link_NAG-ASN : bond 0.00245 / 0.13 ( 1) link_NAG-ASN : angle 1.35850 / 0.73 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.090 Fit side-chains REVERT: C 378 LYS cc_start: 0.8799 (mttm) cc_final: 0.8516 (mtpt) REVERT: C 386 LYS cc_start: 0.8528 (mmtp) cc_final: 0.7464 (ttpt) REVERT: C 403 ARG cc_start: 0.8697 (ptt180) cc_final: 0.8442 (ptt180) REVERT: H 19 ARG cc_start: 0.8646 (ttm-80) cc_final: 0.8061 (ttm110) REVERT: H 22 CYS cc_start: 0.7235 (t) cc_final: 0.6996 (t) REVERT: H 72 ASP cc_start: 0.8364 (t0) cc_final: 0.7966 (t0) REVERT: H 79 TYR cc_start: 0.7990 (m-10) cc_final: 0.7637 (m-10) REVERT: H 113 LEU cc_start: 0.8807 (tt) cc_final: 0.8527 (mp) outliers start: 6 outliers final: 5 residues processed: 74 average time/residue: 0.0927 time to fit residues: 7.6310 Evaluate side-chains 75 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 112 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 23 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 481 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.111208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.093542 restraints weight = 4421.964| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 3.06 r_work: 0.3115 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2540 Z= 0.170 Angle : 0.575 7.335 3460 Z= 0.299 Chirality : 0.044 0.148 364 Planarity : 0.004 0.035 447 Dihedral : 4.777 17.082 348 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.64 % Allowed : 19.62 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.47), residues: 307 helix: -3.14 (0.78), residues: 34 sheet: 0.67 (0.56), residues: 82 loop : -1.19 (0.44), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 19 TYR 0.018 0.001 TYR C 495 PHE 0.012 0.002 PHE C 456 TRP 0.008 0.001 TRP H 36 HIS 0.000 0.000 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 ( 2534) covalent geometry : angle 0.57446 / 0.30 ( 3447) SS BOND : bond 0.00132 / 0.09 ( 5) SS BOND : angle 0.42324 / 0.22 ( 10) hydrogen bonds : bond 0.03248 / 1.94 ( 75) hydrogen bonds : angle 6.23818 / 4.23 ( 204) link_NAG-ASN : bond 0.00256 / 0.13 ( 1) link_NAG-ASN : angle 1.40368 / 0.75 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 902.67 seconds wall clock time: 16 minutes 13.02 seconds (973.02 seconds total)