Starting phenix.real_space_refine on Thu Sep 10 20:00:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6zs5_11388/09_2026/6zs5_11388.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zs5_11388/09_2026/6zs5_11388.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6zs5_11388/09_2026/6zs5_11388.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zs5_11388/09_2026/6zs5_11388.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6zs5_11388/09_2026/6zs5_11388.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6zs5_11388/09_2026/6zs5_11388.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6zs5_11388/09_2026/6zs5_11388.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zs5_11388/09_2026/6zs5_11388.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.082 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 21 5.16 5 C 1261 2.51 5 N 341 2.21 5 O 413 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2036 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 911 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "D" Number of atoms: 1036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1036 Classifications: {'peptide': 141} Incomplete info: {'backbone_only': 12} Link IDs: {'PTRANS': 6, 'TRANS': 134} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 3, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 0.56, per 1000 atoms: 0.28 Number of scatterers: 2036 At special positions: 0 Unit cell: (72.628, 71.544, 88.888, 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 21 16.00 O 413 8.00 N 341 7.00 C 1261 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 335 " - pdb=" SG CYS A 425 " distance=2.03 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS A 389 " distance=2.04 Simple disulfide: pdb=" SG CYS D 506 " - pdb=" SG CYS D 566 " distance=2.03 Simple disulfide: pdb=" SG CYS D 527 " - pdb=" SG CYS D 582 " distance=1.59 Simple disulfide: pdb=" SG CYS D 571 " - pdb=" SG CYS D 578 " distance=1.89 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 ALPHA1-3 " BMA B 3 " - " MAN B 4 " ALPHA1-6 " BMA B 3 " - " MAN B 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG B 1 " - " ASN A 396 " " NAG C 1 " - " ASN D 513 " Time building additional restraints: 0.23 Conformation dependent library (CDL) restraints added in 81.7 milliseconds 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 456 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 43.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.04 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 331 through 333 removed outlier: 3.661A pdb=" N VAL A 342 " --> pdb=" O VAL A 380 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 358 through 360 removed outlier: 3.662A pdb=" N ASN A 404 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE A 419 " --> pdb=" O LEU A 408 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 392 through 395 removed outlier: 3.662A pdb=" N ASN A 404 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE A 419 " --> pdb=" O LEU A 408 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 430 through 434 removed outlier: 6.680A pdb=" N TYR D 563 " --> pdb=" O ALA D 508 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ALA D 508 " --> pdb=" O TYR D 563 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N HIS D 565 " --> pdb=" O CYS D 506 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N CYS D 506 " --> pdb=" O HIS D 565 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLU D 567 " --> pdb=" O THR D 504 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N CYS D 506 " --> pdb=" O ILE D 522 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 438 through 440 removed outlier: 6.863A pdb=" N ALA A 438 " --> pdb=" O VAL D 477 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 458 through 463 removed outlier: 4.017A pdb=" N TYR D 486 " --> pdb=" O PHE D 463 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL D 550 " --> pdb=" O LEU D 485 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ARG D 547 " --> pdb=" O VAL D 538 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL D 538 " --> pdb=" O ARG D 547 " (cutoff:3.500A) 61 hydrogen bonds defined for protein. 162 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: 0.22 Time building geometry restraints manager: 0.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 332 1.31 - 1.44: 558 1.44 - 1.57: 1145 1.57 - 1.70: 3 1.70 - 1.83: 31 Bond restraints: 2069 Sorted by residual: bond pdb=" CA SER D 583 " pdb=" C SER D 583 " ideal model delta sigma weight residual 1.520 1.462 0.059 1.20e-02 6.94e+03 2.41e+01 bond pdb=" C SER D 583 " pdb=" O SER D 583 " ideal model delta sigma weight residual 1.234 1.180 0.055 1.15e-02 7.56e+03 2.28e+01 bond pdb=" CA THR D 581 " pdb=" C THR D 581 " ideal model delta sigma weight residual 1.523 1.484 0.039 1.21e-02 6.83e+03 1.06e+01 bond pdb=" CA SER D 583 " pdb=" CB SER D 583 " ideal model delta sigma weight residual 1.533 1.479 0.054 1.69e-02 3.50e+03 1.02e+01 bond pdb=" N THR D 581 " pdb=" CA THR D 581 " ideal model delta sigma weight residual 1.460 1.423 0.036 1.20e-02 6.94e+03 9.24e+00 ... (remaining 2064 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 2659 2.18 - 4.37: 101 4.37 - 6.55: 28 6.55 - 8.74: 3 8.74 - 10.92: 1 Bond angle restraints: 2792 Sorted by residual: angle pdb=" C LYS D 579 " pdb=" N PRO D 580 " pdb=" CA PRO D 580 " ideal model delta sigma weight residual 119.76 125.33 -5.57 1.03e+00 9.43e-01 2.92e+01 angle pdb=" N GLY A 387 " pdb=" CA GLY A 387 " pdb=" C GLY A 387 " ideal model delta sigma weight residual 112.34 123.26 -10.92 2.04e+00 2.40e-01 2.87e+01 angle pdb=" N THR D 581 " pdb=" CA THR D 581 " pdb=" C THR D 581 " ideal model delta sigma weight residual 108.02 100.12 7.90 1.75e+00 3.27e-01 2.04e+01 angle pdb=" C THR D 581 " pdb=" CA THR D 581 " pdb=" CB THR D 581 " ideal model delta sigma weight residual 110.74 104.22 6.52 1.61e+00 3.86e-01 1.64e+01 angle pdb=" CA PRO D 580 " pdb=" C PRO D 580 " pdb=" N THR D 581 " ideal model delta sigma weight residual 115.56 110.66 4.90 1.27e+00 6.20e-01 1.49e+01 ... (remaining 2787 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 1085 17.90 - 35.79: 87 35.79 - 53.69: 15 53.69 - 71.59: 4 71.59 - 89.48: 2 Dihedral angle restraints: 1193 sinusoidal: 472 harmonic: 721 Sorted by residual: dihedral pdb=" CA LYS A 346 " pdb=" C LYS A 346 " pdb=" N CYS A 347 " pdb=" CA CYS A 347 " ideal model delta harmonic sigma weight residual 180.00 150.31 29.69 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" N THR D 581 " pdb=" C THR D 581 " pdb=" CA THR D 581 " pdb=" CB THR D 581 " ideal model delta harmonic sigma weight residual 123.40 109.35 14.05 0 2.50e+00 1.60e-01 3.16e+01 dihedral pdb=" C THR D 581 " pdb=" N THR D 581 " pdb=" CA THR D 581 " pdb=" CB THR D 581 " ideal model delta harmonic sigma weight residual -122.00 -108.06 -13.94 0 2.50e+00 1.60e-01 3.11e+01 ... (remaining 1190 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 256 0.068 - 0.137: 68 0.137 - 0.205: 4 0.205 - 0.273: 3 0.273 - 0.342: 2 Chirality restraints: 333 Sorted by residual: chirality pdb=" CA THR D 581 " pdb=" N THR D 581 " pdb=" C THR D 581 " pdb=" CB THR D 581 " both_signs ideal model delta sigma weight residual False 2.53 2.87 -0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.62 0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" C2 BMA B 3 " pdb=" C1 BMA B 3 " pdb=" C3 BMA B 3 " pdb=" O2 BMA B 3 " both_signs ideal model delta sigma weight residual False 2.47 2.74 -0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 330 not shown) Planarity restraints: 354 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP D 525 " -0.015 2.00e-02 2.50e+03 3.05e-02 9.30e+00 pdb=" CG ASP D 525 " 0.053 2.00e-02 2.50e+03 pdb=" OD1 ASP D 525 " -0.019 2.00e-02 2.50e+03 pdb=" OD2 ASP D 525 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 386 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.04e+00 pdb=" CG ASP A 386 " 0.042 2.00e-02 2.50e+03 pdb=" OD1 ASP A 386 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP A 386 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 387 " -0.041 5.00e-02 4.00e+02 6.06e-02 5.87e+00 pdb=" N PRO A 388 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 388 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 388 " -0.035 5.00e-02 4.00e+02 ... (remaining 351 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 186 2.74 - 3.28: 1655 3.28 - 3.82: 2977 3.82 - 4.36: 3207 4.36 - 4.90: 5904 Nonbonded interactions: 13929 Sorted by model distance: nonbonded pdb=" O THR D 581 " pdb=" OG1 THR D 581 " model vdw 2.202 3.040 nonbonded pdb=" OD1 ASP D 532 " pdb=" OG1 THR D 534 " model vdw 2.319 3.040 nonbonded pdb=" OG SER A 362 " pdb=" OD1 ASN A 404 " model vdw 2.342 3.040 nonbonded pdb=" OG SER D 543 " pdb=" N SER D 544 " model vdw 2.348 3.120 nonbonded pdb=" OH TYR A 402 " pdb=" OD2 ASP D 495 " model vdw 2.369 3.040 ... (remaining 13924 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.290 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: 0.030 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 3.820 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 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 : 0.013 0.438 2081 Z= 0.660 Angle : 1.367 22.944 2823 Z= 0.691 Chirality : 0.067 0.342 333 Planarity : 0.008 0.061 352 Dihedral : 13.945 89.480 722 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Cbeta Deviations : 0.44 % 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: -2.98 (0.45), residues: 253 helix: None (None), residues: 0 sheet: -1.19 (0.53), residues: 92 loop : -2.61 (0.37), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 395 TYR 0.027 0.003 TYR D 486 PHE 0.024 0.003 PHE A 423 TRP 0.013 0.003 TRP A 377 HIS 0.002 0.001 HIS D 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00847 / 0.43 ( 2069) covalent geometry : angle 1.08744 / 0.59 ( 2792) SS BOND : bond 0.20505 / 10.46 ( 5) SS BOND : angle 11.03486 / 5.55 ( 10) hydrogen bonds : bond 0.28007 / 19.08 ( 53) hydrogen bonds : angle 10.55124 / 6.78 ( 162) link_ALPHA1-3 : bond 0.00788 / 0.41 ( 1) link_ALPHA1-3 : angle 1.61819 / 0.86 ( 3) link_ALPHA1-6 : bond 0.01075 / 0.57 ( 1) link_ALPHA1-6 : angle 1.86495 / 0.86 ( 3) link_BETA1-4 : bond 0.02124 / 1.03 ( 3) link_BETA1-4 : angle 6.23863 / 2.74 ( 9) link_NAG-ASN : bond 0.00391 / 0.19 ( 2) link_NAG-ASN : angle 8.07290 / 3.87 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.086 Fit side-chains REVERT: A 375 ARG cc_start: 0.7475 (mtp180) cc_final: 0.6696 (tpt170) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.0915 time to fit residues: 6.4099 Evaluate side-chains 45 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 11 optimal weight: 0.2980 chunk 18 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 348 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.085339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.072262 restraints weight = 6035.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.074077 restraints weight = 3318.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.075364 restraints weight = 2215.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.076194 restraints weight = 1679.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.076824 restraints weight = 1393.818| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2081 Z= 0.160 Angle : 0.811 11.616 2823 Z= 0.381 Chirality : 0.047 0.169 333 Planarity : 0.005 0.046 352 Dihedral : 5.523 25.621 279 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.65 % Allowed : 22.33 % Favored : 73.02 % 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: -2.23 (0.47), residues: 253 helix: None (None), residues: 0 sheet: -0.43 (0.51), residues: 98 loop : -2.32 (0.42), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 395 TYR 0.015 0.001 TYR D 486 PHE 0.010 0.001 PHE D 548 TRP 0.009 0.002 TRP A 377 HIS 0.001 0.001 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 2069) covalent geometry : angle 0.70819 / 0.36 ( 2792) SS BOND : bond 0.00252 / 0.13 ( 5) SS BOND : angle 1.02823 / 0.44 ( 10) hydrogen bonds : bond 0.04360 / 2.86 ( 53) hydrogen bonds : angle 6.72761 / 4.24 ( 162) link_ALPHA1-3 : bond 0.00665 / 0.35 ( 1) link_ALPHA1-3 : angle 1.06540 / 0.62 ( 3) link_ALPHA1-6 : bond 0.01372 / 0.72 ( 1) link_ALPHA1-6 : angle 1.88008 / 0.78 ( 3) link_BETA1-4 : bond 0.01967 / 0.94 ( 3) link_BETA1-4 : angle 4.76313 / 2.11 ( 9) link_NAG-ASN : bond 0.00337 / 0.18 ( 2) link_NAG-ASN : angle 6.18406 / 2.94 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.127 Fit side-chains REVERT: A 375 ARG cc_start: 0.7394 (mtp180) cc_final: 0.6608 (tpt170) REVERT: A 420 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7679 (ptmt) outliers start: 10 outliers final: 4 residues processed: 52 average time/residue: 0.0642 time to fit residues: 3.8038 Evaluate side-chains 46 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 525 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 10 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 348 GLN D 524 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.084529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.071228 restraints weight = 6178.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.073128 restraints weight = 3364.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.074369 restraints weight = 2225.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.075260 restraints weight = 1689.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.075824 restraints weight = 1394.301| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2081 Z= 0.173 Angle : 0.779 11.848 2823 Z= 0.370 Chirality : 0.047 0.180 333 Planarity : 0.005 0.044 352 Dihedral : 5.201 23.506 279 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 6.51 % Allowed : 20.47 % Favored : 73.02 % 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: -1.96 (0.48), residues: 253 helix: None (None), residues: 0 sheet: -0.17 (0.50), residues: 96 loop : -2.16 (0.43), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 395 TYR 0.019 0.002 TYR D 486 PHE 0.011 0.001 PHE A 423 TRP 0.008 0.002 TRP A 377 HIS 0.001 0.001 HIS D 529 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 ( 2069) covalent geometry : angle 0.68600 / 0.35 ( 2792) SS BOND : bond 0.00105 / 0.05 ( 5) SS BOND : angle 0.82685 / 0.33 ( 10) hydrogen bonds : bond 0.04284 / 2.74 ( 53) hydrogen bonds : angle 6.15936 / 3.94 ( 162) link_ALPHA1-3 : bond 0.00673 / 0.35 ( 1) link_ALPHA1-3 : angle 1.18143 / 0.69 ( 3) link_ALPHA1-6 : bond 0.00983 / 0.52 ( 1) link_ALPHA1-6 : angle 1.70964 / 0.75 ( 3) link_BETA1-4 : bond 0.01780 / 0.85 ( 3) link_BETA1-4 : angle 4.75611 / 2.10 ( 9) link_NAG-ASN : bond 0.00218 / 0.11 ( 2) link_NAG-ASN : angle 5.42118 / 2.58 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.057 Fit side-chains REVERT: A 375 ARG cc_start: 0.7480 (mtp180) cc_final: 0.6747 (tpt170) REVERT: A 420 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7672 (ptmt) REVERT: D 576 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7886 (mp0) outliers start: 14 outliers final: 7 residues processed: 46 average time/residue: 0.0702 time to fit residues: 3.6026 Evaluate side-chains 46 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 525 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 22 optimal weight: 0.8980 chunk 24 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 52.701 > 50:) chunk 18 optimal weight: 0.0000 chunk 23 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 20 optimal weight: 0.7980 overall best weight: 0.5984 ------------------------------------------------------------------------------- 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 = 0.3516 r_free = 0.3516 target = 0.086036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.073130 restraints weight = 6113.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.075064 restraints weight = 3277.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.076390 restraints weight = 2131.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.077289 restraints weight = 1586.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.077891 restraints weight = 1297.530| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2081 Z= 0.123 Angle : 0.738 11.252 2823 Z= 0.343 Chirality : 0.046 0.168 333 Planarity : 0.004 0.041 352 Dihedral : 4.936 20.737 279 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.19 % Allowed : 22.79 % Favored : 73.02 % 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: -1.71 (0.49), residues: 253 helix: None (None), residues: 0 sheet: -0.08 (0.50), residues: 98 loop : -1.95 (0.45), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 395 TYR 0.009 0.001 TYR D 486 PHE 0.009 0.001 PHE A 423 TRP 0.006 0.001 TRP A 377 HIS 0.001 0.001 HIS D 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 2069) covalent geometry : angle 0.65305 / 0.32 ( 2792) SS BOND : bond 0.00134 / 0.07 ( 5) SS BOND : angle 0.60121 / 0.24 ( 10) hydrogen bonds : bond 0.03553 / 2.32 ( 53) hydrogen bonds : angle 5.68151 / 3.70 ( 162) link_ALPHA1-3 : bond 0.00704 / 0.37 ( 1) link_ALPHA1-3 : angle 1.06635 / 0.62 ( 3) link_ALPHA1-6 : bond 0.00925 / 0.49 ( 1) link_ALPHA1-6 : angle 1.64902 / 0.73 ( 3) link_BETA1-4 : bond 0.01796 / 0.86 ( 3) link_BETA1-4 : angle 4.57641 / 2.04 ( 9) link_NAG-ASN : bond 0.00307 / 0.16 ( 2) link_NAG-ASN : angle 4.89945 / 2.40 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.075 Fit side-chains REVERT: A 365 ARG cc_start: 0.8312 (mtm110) cc_final: 0.7905 (mtm110) REVERT: A 375 ARG cc_start: 0.7370 (mtp180) cc_final: 0.6685 (tpt170) REVERT: A 420 LYS cc_start: 0.7876 (ptpt) cc_final: 0.7673 (ptmt) REVERT: A 431 MET cc_start: 0.8850 (mmp) cc_final: 0.8569 (mmp) REVERT: D 576 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8106 (mp0) outliers start: 9 outliers final: 8 residues processed: 46 average time/residue: 0.0534 time to fit residues: 2.8316 Evaluate side-chains 47 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 525 ASP Chi-restraints excluded: chain D residue 560 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 13 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3519 r_free = 0.3519 target = 0.085900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.073139 restraints weight = 6043.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.075049 restraints weight = 3193.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.076362 restraints weight = 2075.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.077199 restraints weight = 1544.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.077799 restraints weight = 1269.357| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2081 Z= 0.128 Angle : 0.736 11.017 2823 Z= 0.339 Chirality : 0.045 0.163 333 Planarity : 0.004 0.039 352 Dihedral : 4.846 19.229 279 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 5.58 % Allowed : 19.53 % Favored : 74.88 % 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: -1.62 (0.49), residues: 253 helix: None (None), residues: 0 sheet: 0.03 (0.51), residues: 98 loop : -1.92 (0.45), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 395 TYR 0.012 0.001 TYR D 486 PHE 0.010 0.001 PHE A 423 TRP 0.007 0.001 TRP A 377 HIS 0.001 0.000 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 2069) covalent geometry : angle 0.65723 / 0.32 ( 2792) SS BOND : bond 0.00078 / 0.04 ( 5) SS BOND : angle 0.48303 / 0.18 ( 10) hydrogen bonds : bond 0.03511 / 2.33 ( 53) hydrogen bonds : angle 5.60656 / 3.70 ( 162) link_ALPHA1-3 : bond 0.00612 / 0.32 ( 1) link_ALPHA1-3 : angle 1.06583 / 0.61 ( 3) link_ALPHA1-6 : bond 0.00902 / 0.47 ( 1) link_ALPHA1-6 : angle 1.61074 / 0.71 ( 3) link_BETA1-4 : bond 0.01722 / 0.82 ( 3) link_BETA1-4 : angle 4.48134 / 2.00 ( 9) link_NAG-ASN : bond 0.00233 / 0.12 ( 2) link_NAG-ASN : angle 4.60563 / 2.27 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.073 Fit side-chains REVERT: A 365 ARG cc_start: 0.8299 (mtm110) cc_final: 0.7882 (mtm110) REVERT: A 375 ARG cc_start: 0.7312 (mtp180) cc_final: 0.6702 (tpt170) REVERT: A 420 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7670 (ptmt) REVERT: A 431 MET cc_start: 0.8887 (mmp) cc_final: 0.8641 (mmp) REVERT: D 531 ARG cc_start: 0.7048 (tpm170) cc_final: 0.6823 (tpm170) REVERT: D 576 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8134 (mp0) outliers start: 12 outliers final: 10 residues processed: 46 average time/residue: 0.0635 time to fit residues: 3.3168 Evaluate side-chains 50 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 525 ASP Chi-restraints excluded: chain D residue 560 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 20 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3505 r_free = 0.3505 target = 0.085200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.072506 restraints weight = 5942.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.074389 restraints weight = 3182.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.075619 restraints weight = 2074.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.076477 restraints weight = 1559.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.077008 restraints weight = 1286.453| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2081 Z= 0.141 Angle : 0.710 10.795 2823 Z= 0.330 Chirality : 0.045 0.157 333 Planarity : 0.004 0.040 352 Dihedral : 4.817 17.986 279 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 6.51 % Allowed : 20.00 % Favored : 73.49 % 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: -1.56 (0.50), residues: 253 helix: None (None), residues: 0 sheet: 0.28 (0.54), residues: 91 loop : -1.95 (0.44), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 395 TYR 0.016 0.001 TYR D 486 PHE 0.009 0.001 PHE A 423 TRP 0.007 0.002 TRP A 377 HIS 0.001 0.000 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 2069) covalent geometry : angle 0.63372 / 0.31 ( 2792) SS BOND : bond 0.00175 / 0.09 ( 5) SS BOND : angle 0.52056 / 0.18 ( 10) hydrogen bonds : bond 0.03452 / 2.30 ( 53) hydrogen bonds : angle 5.32085 / 3.49 ( 162) link_ALPHA1-3 : bond 0.00568 / 0.30 ( 1) link_ALPHA1-3 : angle 1.08604 / 0.60 ( 3) link_ALPHA1-6 : bond 0.00856 / 0.45 ( 1) link_ALPHA1-6 : angle 1.54403 / 0.69 ( 3) link_BETA1-4 : bond 0.01645 / 0.79 ( 3) link_BETA1-4 : angle 4.37871 / 1.95 ( 9) link_NAG-ASN : bond 0.00207 / 0.10 ( 2) link_NAG-ASN : angle 4.42816 / 2.18 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 40 time to evaluate : 0.054 Fit side-chains REVERT: A 365 ARG cc_start: 0.8275 (mtm110) cc_final: 0.7859 (mtm110) REVERT: A 375 ARG cc_start: 0.7346 (mtp180) cc_final: 0.6730 (tpt170) outliers start: 14 outliers final: 9 residues processed: 49 average time/residue: 0.0658 time to fit residues: 3.7248 Evaluate side-chains 45 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 560 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 18 optimal weight: 0.4980 chunk 15 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3531 r_free = 0.3531 target = 0.086347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.073105 restraints weight = 5991.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.075104 restraints weight = 3137.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.076411 restraints weight = 2043.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.077278 restraints weight = 1539.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.077799 restraints weight = 1275.788| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2081 Z= 0.124 Angle : 0.720 10.601 2823 Z= 0.331 Chirality : 0.044 0.158 333 Planarity : 0.003 0.042 352 Dihedral : 4.693 17.569 279 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 5.58 % Allowed : 22.33 % Favored : 72.09 % 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: -1.43 (0.50), residues: 253 helix: None (None), residues: 0 sheet: 0.36 (0.55), residues: 91 loop : -1.85 (0.44), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 395 TYR 0.011 0.001 TYR D 486 PHE 0.009 0.001 PHE A 423 TRP 0.007 0.002 TRP A 377 HIS 0.001 0.000 HIS D 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 2069) covalent geometry : angle 0.64935 / 0.32 ( 2792) SS BOND : bond 0.00068 / 0.03 ( 5) SS BOND : angle 0.43832 / 0.15 ( 10) hydrogen bonds : bond 0.03130 / 2.09 ( 53) hydrogen bonds : angle 5.37208 / 3.54 ( 162) link_ALPHA1-3 : bond 0.00537 / 0.28 ( 1) link_ALPHA1-3 : angle 1.06904 / 0.59 ( 3) link_ALPHA1-6 : bond 0.00818 / 0.43 ( 1) link_ALPHA1-6 : angle 1.53326 / 0.68 ( 3) link_BETA1-4 : bond 0.01649 / 0.79 ( 3) link_BETA1-4 : angle 4.32520 / 1.94 ( 9) link_NAG-ASN : bond 0.00227 / 0.12 ( 2) link_NAG-ASN : angle 4.18252 / 2.09 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.049 Fit side-chains REVERT: A 365 ARG cc_start: 0.8238 (mtm110) cc_final: 0.7838 (mtm110) REVERT: A 375 ARG cc_start: 0.7396 (mtp180) cc_final: 0.6781 (tpt170) REVERT: A 431 MET cc_start: 0.8881 (mmp) cc_final: 0.8624 (mmp) REVERT: D 576 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8232 (mp0) outliers start: 12 outliers final: 10 residues processed: 50 average time/residue: 0.0651 time to fit residues: 3.7074 Evaluate side-chains 50 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 525 ASP Chi-restraints excluded: chain D residue 560 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 11 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 1 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 18 optimal weight: 0.1980 chunk 13 optimal weight: 0.3980 chunk 9 optimal weight: 0.8980 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 = 0.3520 r_free = 0.3520 target = 0.085951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.073124 restraints weight = 6000.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.075054 restraints weight = 3127.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.076363 restraints weight = 2019.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.077236 restraints weight = 1504.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.077751 restraints weight = 1229.422| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2081 Z= 0.116 Angle : 0.707 10.339 2823 Z= 0.325 Chirality : 0.045 0.156 333 Planarity : 0.003 0.040 352 Dihedral : 4.634 17.814 279 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.65 % Allowed : 25.58 % Favored : 69.77 % 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: -1.74 (0.49), residues: 253 helix: -3.99 (0.86), residues: 6 sheet: 0.23 (0.54), residues: 90 loop : -2.01 (0.44), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 459 TYR 0.008 0.001 TYR D 486 PHE 0.009 0.001 PHE A 423 TRP 0.006 0.001 TRP A 377 HIS 0.001 0.000 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 2069) covalent geometry : angle 0.63843 / 0.31 ( 2792) SS BOND : bond 0.00062 / 0.03 ( 5) SS BOND : angle 0.43591 / 0.18 ( 10) hydrogen bonds : bond 0.03135 / 2.10 ( 53) hydrogen bonds : angle 5.31592 / 3.51 ( 162) link_ALPHA1-3 : bond 0.00573 / 0.30 ( 1) link_ALPHA1-3 : angle 1.06744 / 0.58 ( 3) link_ALPHA1-6 : bond 0.00807 / 0.42 ( 1) link_ALPHA1-6 : angle 1.50758 / 0.67 ( 3) link_BETA1-4 : bond 0.01603 / 0.77 ( 3) link_BETA1-4 : angle 4.25421 / 1.92 ( 9) link_NAG-ASN : bond 0.00219 / 0.11 ( 2) link_NAG-ASN : angle 4.01459 / 2.02 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.083 Fit side-chains REVERT: A 365 ARG cc_start: 0.8230 (mtm110) cc_final: 0.7839 (mtm110) REVERT: A 375 ARG cc_start: 0.7391 (mtp180) cc_final: 0.6773 (tpt170) REVERT: A 431 MET cc_start: 0.8881 (mmp) cc_final: 0.8611 (mmp) REVERT: D 576 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8195 (mp0) outliers start: 10 outliers final: 7 residues processed: 48 average time/residue: 0.0720 time to fit residues: 3.9830 Evaluate side-chains 46 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 560 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 18 optimal weight: 0.5980 chunk 5 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3517 r_free = 0.3517 target = 0.085826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.072881 restraints weight = 5956.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.074877 restraints weight = 3090.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.076199 restraints weight = 1993.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.077052 restraints weight = 1484.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.077614 restraints weight = 1232.140| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2081 Z= 0.123 Angle : 0.699 10.137 2823 Z= 0.323 Chirality : 0.044 0.151 333 Planarity : 0.003 0.041 352 Dihedral : 4.584 18.645 279 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.72 % Allowed : 26.05 % Favored : 70.23 % 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: -1.81 (0.49), residues: 253 helix: -4.12 (0.71), residues: 6 sheet: 0.22 (0.54), residues: 90 loop : -2.07 (0.44), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 459 TYR 0.011 0.001 TYR D 486 PHE 0.008 0.001 PHE A 423 TRP 0.006 0.001 TRP A 377 HIS 0.001 0.000 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 2069) covalent geometry : angle 0.63157 / 0.31 ( 2792) SS BOND : bond 0.00049 / 0.02 ( 5) SS BOND : angle 0.51531 / 0.21 ( 10) hydrogen bonds : bond 0.03133 / 2.13 ( 53) hydrogen bonds : angle 5.30310 / 3.46 ( 162) link_ALPHA1-3 : bond 0.00539 / 0.28 ( 1) link_ALPHA1-3 : angle 1.09560 / 0.59 ( 3) link_ALPHA1-6 : bond 0.00801 / 0.42 ( 1) link_ALPHA1-6 : angle 1.47543 / 0.66 ( 3) link_BETA1-4 : bond 0.01542 / 0.74 ( 3) link_BETA1-4 : angle 4.18383 / 1.89 ( 9) link_NAG-ASN : bond 0.00186 / 0.10 ( 2) link_NAG-ASN : angle 3.94733 / 1.98 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.050 Fit side-chains REVERT: A 340 MET cc_start: 0.8374 (mmm) cc_final: 0.8089 (mtt) REVERT: A 365 ARG cc_start: 0.8253 (mtm110) cc_final: 0.7883 (mtm110) REVERT: A 375 ARG cc_start: 0.7519 (mtp180) cc_final: 0.6834 (tpt170) REVERT: A 431 MET cc_start: 0.8870 (mmp) cc_final: 0.8625 (mmp) REVERT: D 576 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8193 (mp0) outliers start: 8 outliers final: 7 residues processed: 47 average time/residue: 0.0773 time to fit residues: 4.1001 Evaluate side-chains 47 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 560 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 21 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 20 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3529 r_free = 0.3529 target = 0.086378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.073134 restraints weight = 5990.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.075150 restraints weight = 3122.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.076507 restraints weight = 2027.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.077377 restraints weight = 1524.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.077939 restraints weight = 1272.060| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2081 Z= 0.125 Angle : 0.730 10.021 2823 Z= 0.337 Chirality : 0.044 0.150 333 Planarity : 0.003 0.040 352 Dihedral : 4.540 17.605 279 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.72 % Allowed : 27.44 % Favored : 68.84 % 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: -1.83 (0.49), residues: 253 helix: -3.74 (1.07), residues: 6 sheet: 0.14 (0.53), residues: 90 loop : -2.07 (0.44), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 395 TYR 0.011 0.001 TYR D 486 PHE 0.009 0.001 PHE A 423 TRP 0.007 0.001 TRP A 377 HIS 0.001 0.000 HIS D 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 ( 2069) covalent geometry : angle 0.66770 / 0.32 ( 2792) SS BOND : bond 0.00051 / 0.03 ( 5) SS BOND : angle 0.61190 / 0.23 ( 10) hydrogen bonds : bond 0.03112 / 2.13 ( 53) hydrogen bonds : angle 5.33637 / 3.46 ( 162) link_ALPHA1-3 : bond 0.00503 / 0.26 ( 1) link_ALPHA1-3 : angle 1.11542 / 0.59 ( 3) link_ALPHA1-6 : bond 0.00777 / 0.41 ( 1) link_ALPHA1-6 : angle 1.45295 / 0.65 ( 3) link_BETA1-4 : bond 0.01523 / 0.73 ( 3) link_BETA1-4 : angle 4.13991 / 1.87 ( 9) link_NAG-ASN : bond 0.00175 / 0.09 ( 2) link_NAG-ASN : angle 3.89274 / 1.95 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.049 Fit side-chains REVERT: A 340 MET cc_start: 0.8438 (mmm) cc_final: 0.8144 (mtt) REVERT: A 365 ARG cc_start: 0.8190 (mtm110) cc_final: 0.7829 (mtm110) REVERT: A 375 ARG cc_start: 0.7479 (mtp180) cc_final: 0.6855 (tpt170) REVERT: A 431 MET cc_start: 0.8857 (mmp) cc_final: 0.8626 (mmp) REVERT: D 567 GLU cc_start: 0.7834 (pm20) cc_final: 0.7433 (pm20) REVERT: D 576 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8204 (mp0) outliers start: 8 outliers final: 8 residues processed: 45 average time/residue: 0.0729 time to fit residues: 3.7086 Evaluate side-chains 47 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 560 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 17 optimal weight: 0.0670 chunk 23 optimal weight: 0.9980 chunk 24 optimal weight: 0.0980 chunk 3 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 = 0.3537 r_free = 0.3537 target = 0.086743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.073747 restraints weight = 6114.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.075805 restraints weight = 3114.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.077171 restraints weight = 1988.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.078052 restraints weight = 1474.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.078585 restraints weight = 1210.771| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2081 Z= 0.110 Angle : 0.702 9.762 2823 Z= 0.322 Chirality : 0.044 0.148 333 Planarity : 0.003 0.039 352 Dihedral : 4.393 16.680 279 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.19 % Allowed : 27.44 % Favored : 68.37 % 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: -1.71 (0.49), residues: 253 helix: -3.23 (1.63), residues: 6 sheet: 0.26 (0.54), residues: 90 loop : -2.03 (0.44), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 395 TYR 0.007 0.001 TYR D 486 PHE 0.008 0.001 PHE A 423 TRP 0.006 0.001 TRP A 377 HIS 0.002 0.001 HIS D 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 2069) covalent geometry : angle 0.64098 / 0.31 ( 2792) SS BOND : bond 0.00058 / 0.03 ( 5) SS BOND : angle 0.51126 / 0.20 ( 10) hydrogen bonds : bond 0.02917 / 2.00 ( 53) hydrogen bonds : angle 5.23085 / 3.38 ( 162) link_ALPHA1-3 : bond 0.00463 / 0.24 ( 1) link_ALPHA1-3 : angle 1.06576 / 0.57 ( 3) link_ALPHA1-6 : bond 0.00777 / 0.41 ( 1) link_ALPHA1-6 : angle 1.45126 / 0.64 ( 3) link_BETA1-4 : bond 0.01504 / 0.72 ( 3) link_BETA1-4 : angle 4.06533 / 1.85 ( 9) link_NAG-ASN : bond 0.00211 / 0.11 ( 2) link_NAG-ASN : angle 3.71474 / 1.88 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 631.23 seconds wall clock time: 11 minutes 30.56 seconds (690.56 seconds total)