Starting phenix.real_space_refine on Tue Mar 3 11:30:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cud_26998/03_2026/8cud_26998.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cud_26998/03_2026/8cud_26998.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cud_26998/03_2026/8cud_26998.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cud_26998/03_2026/8cud_26998.map" model { file = "/net/cci-nas-00/data/ceres_data/8cud_26998/03_2026/8cud_26998.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cud_26998/03_2026/8cud_26998.cif" } resolution = 2.94 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= 0.004 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 2153 2.51 5 N 526 2.21 5 O 594 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-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3294 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3292 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 12, 'TRANS': 420} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 0.80, per 1000 atoms: 0.24 Number of scatterers: 3294 At special positions: 0 Unit cell: (71.568, 66.456, 80.088, 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 594 8.00 N 526 7.00 C 2153 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 0.23 Conformation dependent library (CDL) restraints added in 273.3 milliseconds 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 800 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 1 sheets defined 81.5% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 19 through 42 removed outlier: 3.604A pdb=" N ILE A 32 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR A 33 " --> pdb=" O VAL A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 52 removed outlier: 3.520A pdb=" N PHE A 52 " --> pdb=" O GLU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 64 Processing helix chain 'A' and resid 66 through 82 removed outlier: 3.888A pdb=" N LEU A 82 " --> pdb=" O GLY A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 117 removed outlier: 3.673A pdb=" N GLY A 88 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS A 89 " --> pdb=" O ASN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 150 removed outlier: 3.551A pdb=" N LEU A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE A 146 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 158 Processing helix chain 'A' and resid 211 through 228 removed outlier: 3.659A pdb=" N LYS A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 232 removed outlier: 3.616A pdb=" N LYS A 232 " --> pdb=" O MET A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 229 through 232' Processing helix chain 'A' and resid 233 through 270 removed outlier: 3.596A pdb=" N VAL A 251 " --> pdb=" O THR A 247 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLN A 252 " --> pdb=" O MET A 248 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE A 253 " --> pdb=" O LYS A 249 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TRP A 256 " --> pdb=" O GLN A 252 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N TYR A 257 " --> pdb=" O ILE A 253 " (cutoff:3.500A) Proline residue: A 259 - end of helix removed outlier: 3.644A pdb=" N GLY A 268 " --> pdb=" O PHE A 264 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE A 270 " --> pdb=" O ILE A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 282 Processing helix chain 'A' and resid 282 through 299 Processing helix chain 'A' and resid 299 through 309 Processing helix chain 'A' and resid 312 through 319 removed outlier: 4.157A pdb=" N PHE A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 331 Processing helix chain 'A' and resid 336 through 348 removed outlier: 3.517A pdb=" N ASN A 348 " --> pdb=" O ALA A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 366 removed outlier: 4.179A pdb=" N PHE A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Proline residue: A 360 - end of helix removed outlier: 4.032A pdb=" N THR A 364 " --> pdb=" O PRO A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 385 Processing helix chain 'A' and resid 390 through 408 removed outlier: 3.796A pdb=" N ILE A 406 " --> pdb=" O THR A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 427 removed outlier: 3.648A pdb=" N VAL A 417 " --> pdb=" O GLN A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 432 removed outlier: 3.678A pdb=" N ASP A 432 " --> pdb=" O PRO A 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 429 through 432' Processing helix chain 'A' and resid 433 through 438 removed outlier: 3.623A pdb=" N ILE A 437 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ALA A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 433 through 438' Processing helix chain 'A' and resid 442 through 466 removed outlier: 3.802A pdb=" N PHE A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG A 447 " --> pdb=" O LEU A 443 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N THR A 448 " --> pdb=" O ASP A 444 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N MET A 449 " --> pdb=" O ARG A 445 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL A 450 " --> pdb=" O PHE A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 473 Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 167 229 hydrogen bonds defined for protein. 681 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: 0.32 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: 936 1.34 - 1.45: 415 1.45 - 1.57: 1951 1.57 - 1.69: 0 1.69 - 1.81: 39 Bond restraints: 3341 Sorted by residual: bond pdb=" N VAL A 113 " pdb=" CA VAL A 113 " ideal model delta sigma weight residual 1.460 1.497 -0.037 1.21e-02 6.83e+03 9.47e+00 bond pdb=" N MET A 367 " pdb=" CA MET A 367 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.14e-02 7.69e+03 9.37e+00 bond pdb=" N ILE A 210 " pdb=" CA ILE A 210 " ideal model delta sigma weight residual 1.458 1.496 -0.039 1.27e-02 6.20e+03 9.33e+00 bond pdb=" N ILE A 116 " pdb=" CA ILE A 116 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.19e-02 7.06e+03 9.16e+00 bond pdb=" N ILE A 365 " pdb=" CA ILE A 365 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.30e-02 5.92e+03 8.98e+00 ... (remaining 3336 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.99: 4143 0.99 - 1.98: 248 1.98 - 2.97: 106 2.97 - 3.96: 27 3.96 - 4.95: 12 Bond angle restraints: 4536 Sorted by residual: angle pdb=" CA ASP A 368 " pdb=" C ASP A 368 " pdb=" O ASP A 368 " ideal model delta sigma weight residual 121.07 116.89 4.18 1.10e+00 8.26e-01 1.44e+01 angle pdb=" CA ILE A 116 " pdb=" C ILE A 116 " pdb=" O ILE A 116 " ideal model delta sigma weight residual 120.95 117.14 3.81 1.04e+00 9.25e-01 1.34e+01 angle pdb=" CA THR A 448 " pdb=" C THR A 448 " pdb=" O THR A 448 " ideal model delta sigma weight residual 120.82 117.18 3.64 1.05e+00 9.07e-01 1.21e+01 angle pdb=" N ARG A 315 " pdb=" CA ARG A 315 " pdb=" C ARG A 315 " ideal model delta sigma weight residual 111.36 107.59 3.77 1.09e+00 8.42e-01 1.20e+01 angle pdb=" C GLY A 369 " pdb=" N THR A 370 " pdb=" CA THR A 370 " ideal model delta sigma weight residual 120.54 125.06 -4.52 1.35e+00 5.49e-01 1.12e+01 ... (remaining 4531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 1765 17.91 - 35.83: 182 35.83 - 53.74: 44 53.74 - 71.65: 6 71.65 - 89.57: 4 Dihedral angle restraints: 2001 sinusoidal: 760 harmonic: 1241 Sorted by residual: dihedral pdb=" CA GLU A 40 " pdb=" C GLU A 40 " pdb=" N HIS A 41 " pdb=" CA HIS A 41 " ideal model delta harmonic sigma weight residual 180.00 -163.09 -16.91 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CB GLU A 463 " pdb=" CG GLU A 463 " pdb=" CD GLU A 463 " pdb=" OE1 GLU A 463 " ideal model delta sinusoidal sigma weight residual 0.00 -89.57 89.57 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" C ASP A 368 " pdb=" N ASP A 368 " pdb=" CA ASP A 368 " pdb=" CB ASP A 368 " ideal model delta harmonic sigma weight residual -122.60 -130.60 8.00 0 2.50e+00 1.60e-01 1.03e+01 ... (remaining 1998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 405 0.042 - 0.083: 111 0.083 - 0.125: 40 0.125 - 0.166: 14 0.166 - 0.208: 5 Chirality restraints: 575 Sorted by residual: chirality pdb=" CA ASP A 368 " pdb=" N ASP A 368 " pdb=" C ASP A 368 " pdb=" CB ASP A 368 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CB VAL A 113 " pdb=" CA VAL A 113 " pdb=" CG1 VAL A 113 " pdb=" CG2 VAL A 113 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA MET A 318 " pdb=" N MET A 318 " pdb=" C MET A 318 " pdb=" CB MET A 318 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.38e-01 ... (remaining 572 not shown) Planarity restraints: 555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 364 " -0.010 2.00e-02 2.50e+03 2.05e-02 4.21e+00 pdb=" C THR A 364 " 0.035 2.00e-02 2.50e+03 pdb=" O THR A 364 " -0.013 2.00e-02 2.50e+03 pdb=" N ILE A 365 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 411 " 0.021 5.00e-02 4.00e+02 3.21e-02 1.65e+00 pdb=" N PRO A 412 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 412 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 412 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 66 " 0.006 2.00e-02 2.50e+03 1.15e-02 1.31e+00 pdb=" C ILE A 66 " -0.020 2.00e-02 2.50e+03 pdb=" O ILE A 66 " 0.007 2.00e-02 2.50e+03 pdb=" N ILE A 67 " 0.007 2.00e-02 2.50e+03 ... (remaining 552 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.93: 1340 2.93 - 3.42: 3473 3.42 - 3.91: 5224 3.91 - 4.41: 5551 4.41 - 4.90: 9805 Nonbonded interactions: 25393 Sorted by model distance: nonbonded pdb=" O PRO A 69 " pdb=" OG SER A 73 " model vdw 2.433 3.040 nonbonded pdb=" OE2 GLU A 345 " pdb=" NH1 ARG A 356 " model vdw 2.437 3.120 nonbonded pdb=" O SER A 331 " pdb=" OG SER A 331 " model vdw 2.535 3.040 nonbonded pdb=" OD1 ASN A 312 " pdb=" N PHE A 314 " model vdw 2.547 3.120 nonbonded pdb=" OH TYR A 373 " pdb=" OD1 ASP A 440 " model vdw 2.554 3.040 ... (remaining 25388 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.550 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: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.060 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 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 : 0.005 0.072 3341 Z= 0.353 Angle : 0.667 4.948 4536 Z= 0.466 Chirality : 0.049 0.208 575 Planarity : 0.004 0.032 555 Dihedral : 15.611 89.566 1201 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.00 % Allowed : 22.99 % Favored : 77.01 % 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: 1.42 (0.42), residues: 429 helix: 1.51 (0.31), residues: 320 sheet: 1.60 (1.19), residues: 16 loop : -1.08 (0.56), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 447 TYR 0.010 0.001 TYR A 97 PHE 0.011 0.001 PHE A 457 TRP 0.004 0.001 TRP A 19 HIS 0.002 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00490 ( 3341) covalent geometry : angle 0.66677 ( 4536) hydrogen bonds : bond 0.17492 ( 229) hydrogen bonds : angle 5.58415 ( 681) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.117 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.4911 time to fit residues: 29.3700 Evaluate side-chains 47 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.176850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.127942 restraints weight = 3927.724| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.75 r_work: 0.3234 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3341 Z= 0.130 Angle : 0.486 5.532 4536 Z= 0.257 Chirality : 0.038 0.142 575 Planarity : 0.004 0.031 555 Dihedral : 3.507 14.388 455 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.88 % Allowed : 22.16 % Favored : 73.96 % 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: 1.77 (0.42), residues: 429 helix: 1.89 (0.31), residues: 321 sheet: 1.96 (1.23), residues: 16 loop : -1.62 (0.57), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 447 TYR 0.010 0.001 TYR A 373 PHE 0.013 0.001 PHE A 341 TRP 0.003 0.001 TRP A 19 HIS 0.002 0.001 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 3341) covalent geometry : angle 0.48572 ( 4536) hydrogen bonds : bond 0.05312 ( 229) hydrogen bonds : angle 4.28898 ( 681) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.120 Fit side-chains REVERT: A 231 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7232 (tp30) REVERT: A 367 MET cc_start: 0.7636 (mmt) cc_final: 0.7421 (mmp) REVERT: A 428 LEU cc_start: 0.6965 (OUTLIER) cc_final: 0.6692 (mt) outliers start: 14 outliers final: 4 residues processed: 61 average time/residue: 0.4462 time to fit residues: 28.1689 Evaluate side-chains 51 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 9 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.173014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.123492 restraints weight = 3883.019| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.78 r_work: 0.3174 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3341 Z= 0.182 Angle : 0.554 6.991 4536 Z= 0.291 Chirality : 0.041 0.240 575 Planarity : 0.004 0.033 555 Dihedral : 3.724 15.501 455 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 5.54 % Allowed : 21.05 % Favored : 73.41 % 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: 1.34 (0.42), residues: 429 helix: 1.68 (0.30), residues: 314 sheet: 1.83 (1.21), residues: 16 loop : -1.93 (0.56), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 447 TYR 0.011 0.002 TYR A 98 PHE 0.014 0.002 PHE A 341 TRP 0.003 0.001 TRP A 19 HIS 0.001 0.001 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 3341) covalent geometry : angle 0.55447 ( 4536) hydrogen bonds : bond 0.06360 ( 229) hydrogen bonds : angle 4.35627 ( 681) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 47 time to evaluate : 0.129 Fit side-chains REVERT: A 200 TYR cc_start: 0.8161 (m-10) cc_final: 0.7787 (m-10) REVERT: A 315 ARG cc_start: 0.6694 (mtt-85) cc_final: 0.6002 (mmm-85) REVERT: A 428 LEU cc_start: 0.6925 (OUTLIER) cc_final: 0.6598 (mp) outliers start: 20 outliers final: 7 residues processed: 62 average time/residue: 0.4619 time to fit residues: 29.6370 Evaluate side-chains 54 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 6 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 24 optimal weight: 0.4980 chunk 11 optimal weight: 0.0370 chunk 26 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.176628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.127669 restraints weight = 3839.320| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.74 r_work: 0.3228 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3341 Z= 0.113 Angle : 0.455 5.137 4536 Z= 0.241 Chirality : 0.038 0.174 575 Planarity : 0.003 0.042 555 Dihedral : 3.456 14.998 455 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 5.26 % Allowed : 21.88 % Favored : 72.85 % 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: 1.84 (0.42), residues: 429 helix: 1.92 (0.30), residues: 321 sheet: 2.13 (1.27), residues: 16 loop : -1.56 (0.58), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 447 TYR 0.012 0.001 TYR A 373 PHE 0.014 0.001 PHE A 341 TRP 0.002 0.001 TRP A 19 HIS 0.001 0.000 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 3341) covalent geometry : angle 0.45526 ( 4536) hydrogen bonds : bond 0.04688 ( 229) hydrogen bonds : angle 4.05021 ( 681) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 47 time to evaluate : 0.127 Fit side-chains REVERT: A 200 TYR cc_start: 0.8089 (m-10) cc_final: 0.7675 (m-10) REVERT: A 231 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7253 (tp30) REVERT: A 428 LEU cc_start: 0.6927 (OUTLIER) cc_final: 0.6591 (mp) outliers start: 19 outliers final: 5 residues processed: 62 average time/residue: 0.4165 time to fit residues: 26.7640 Evaluate side-chains 48 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 29 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN ** A 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.175772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.126714 restraints weight = 3827.539| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.74 r_work: 0.3211 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3341 Z= 0.123 Angle : 0.492 7.611 4536 Z= 0.255 Chirality : 0.040 0.232 575 Planarity : 0.004 0.046 555 Dihedral : 3.462 14.152 455 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 4.43 % Allowed : 24.10 % Favored : 71.47 % 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: 1.73 (0.42), residues: 429 helix: 1.91 (0.30), residues: 317 sheet: 2.41 (1.43), residues: 16 loop : -1.77 (0.55), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 447 TYR 0.013 0.001 TYR A 373 PHE 0.012 0.001 PHE A 341 TRP 0.002 0.001 TRP A 19 HIS 0.001 0.000 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 3341) covalent geometry : angle 0.49171 ( 4536) hydrogen bonds : bond 0.04927 ( 229) hydrogen bonds : angle 4.11225 ( 681) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 45 time to evaluate : 0.130 Fit side-chains REVERT: A 200 TYR cc_start: 0.8118 (m-10) cc_final: 0.7719 (m-10) REVERT: A 231 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7291 (tp30) REVERT: A 428 LEU cc_start: 0.6888 (OUTLIER) cc_final: 0.6526 (mp) outliers start: 16 outliers final: 7 residues processed: 57 average time/residue: 0.4442 time to fit residues: 26.2734 Evaluate side-chains 51 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 27 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 26 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.177652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.128182 restraints weight = 3838.788| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.75 r_work: 0.3232 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3341 Z= 0.116 Angle : 0.467 5.986 4536 Z= 0.245 Chirality : 0.039 0.171 575 Planarity : 0.004 0.047 555 Dihedral : 3.415 14.307 455 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 4.16 % Allowed : 25.21 % Favored : 70.64 % 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: 1.79 (0.42), residues: 429 helix: 1.96 (0.31), residues: 317 sheet: 2.50 (1.39), residues: 16 loop : -1.79 (0.55), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 447 TYR 0.013 0.001 TYR A 373 PHE 0.011 0.001 PHE A 341 TRP 0.002 0.001 TRP A 19 HIS 0.001 0.000 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 3341) covalent geometry : angle 0.46737 ( 4536) hydrogen bonds : bond 0.04663 ( 229) hydrogen bonds : angle 4.00339 ( 681) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 0.107 Fit side-chains REVERT: A 200 TYR cc_start: 0.8107 (m-10) cc_final: 0.7707 (m-10) REVERT: A 231 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7310 (tp30) REVERT: A 428 LEU cc_start: 0.6859 (OUTLIER) cc_final: 0.6499 (mp) outliers start: 15 outliers final: 6 residues processed: 56 average time/residue: 0.4415 time to fit residues: 25.5688 Evaluate side-chains 52 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 42 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 3 optimal weight: 0.0030 chunk 24 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 41 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.177572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.130818 restraints weight = 3877.137| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.94 r_work: 0.3219 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3341 Z= 0.113 Angle : 0.470 6.195 4536 Z= 0.244 Chirality : 0.040 0.281 575 Planarity : 0.003 0.048 555 Dihedral : 3.357 14.016 455 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.88 % Allowed : 25.21 % Favored : 70.91 % 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: 1.97 (0.42), residues: 429 helix: 2.03 (0.30), residues: 321 sheet: 2.56 (1.41), residues: 16 loop : -1.61 (0.55), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 447 TYR 0.014 0.001 TYR A 373 PHE 0.012 0.001 PHE A 341 TRP 0.001 0.000 TRP A 19 HIS 0.001 0.000 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 3341) covalent geometry : angle 0.46979 ( 4536) hydrogen bonds : bond 0.04476 ( 229) hydrogen bonds : angle 4.06209 ( 681) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.113 Fit side-chains REVERT: A 200 TYR cc_start: 0.8121 (m-10) cc_final: 0.7721 (m-10) REVERT: A 231 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7272 (tp30) REVERT: A 428 LEU cc_start: 0.6850 (OUTLIER) cc_final: 0.6460 (mp) outliers start: 14 outliers final: 6 residues processed: 56 average time/residue: 0.3994 time to fit residues: 23.2694 Evaluate side-chains 52 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 39 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 0.3980 chunk 41 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 41 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.177281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.126186 restraints weight = 3967.320| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.88 r_work: 0.3227 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3341 Z= 0.114 Angle : 0.467 5.209 4536 Z= 0.244 Chirality : 0.039 0.229 575 Planarity : 0.004 0.049 555 Dihedral : 3.363 13.850 455 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.88 % Allowed : 25.48 % Favored : 70.64 % 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: 1.87 (0.42), residues: 429 helix: 2.04 (0.30), residues: 317 sheet: 2.50 (1.44), residues: 16 loop : -1.85 (0.54), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 447 TYR 0.015 0.001 TYR A 373 PHE 0.010 0.001 PHE A 341 TRP 0.002 0.001 TRP A 19 HIS 0.001 0.000 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 3341) covalent geometry : angle 0.46657 ( 4536) hydrogen bonds : bond 0.04537 ( 229) hydrogen bonds : angle 3.98823 ( 681) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.123 Fit side-chains REVERT: A 200 TYR cc_start: 0.8116 (m-10) cc_final: 0.7718 (m-10) REVERT: A 231 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7296 (tp30) REVERT: A 315 ARG cc_start: 0.6778 (mtt-85) cc_final: 0.6386 (mmm-85) REVERT: A 428 LEU cc_start: 0.6836 (OUTLIER) cc_final: 0.6450 (mp) outliers start: 14 outliers final: 8 residues processed: 57 average time/residue: 0.4726 time to fit residues: 27.8270 Evaluate side-chains 55 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 6.9990 chunk 3 optimal weight: 0.0980 chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 13 optimal weight: 0.0010 chunk 5 optimal weight: 0.0060 chunk 11 optimal weight: 0.9980 overall best weight: 0.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 41 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.179466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.129105 restraints weight = 3854.922| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.84 r_work: 0.3276 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3341 Z= 0.097 Angle : 0.438 5.086 4536 Z= 0.228 Chirality : 0.038 0.166 575 Planarity : 0.003 0.049 555 Dihedral : 3.207 14.350 455 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.49 % Allowed : 26.87 % Favored : 70.64 % 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: 2.12 (0.43), residues: 429 helix: 2.08 (0.30), residues: 329 sheet: 1.43 (1.49), residues: 18 loop : -1.47 (0.59), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 447 TYR 0.017 0.001 TYR A 373 PHE 0.010 0.001 PHE A 341 TRP 0.003 0.000 TRP A 256 HIS 0.001 0.000 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00186 ( 3341) covalent geometry : angle 0.43811 ( 4536) hydrogen bonds : bond 0.03636 ( 229) hydrogen bonds : angle 3.82142 ( 681) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.121 Fit side-chains REVERT: A 200 TYR cc_start: 0.8077 (m-10) cc_final: 0.7682 (m-10) REVERT: A 231 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.7011 (tp30) REVERT: A 428 LEU cc_start: 0.6741 (OUTLIER) cc_final: 0.6309 (mp) outliers start: 9 outliers final: 6 residues processed: 59 average time/residue: 0.4022 time to fit residues: 24.5920 Evaluate side-chains 54 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 13 optimal weight: 0.1980 chunk 11 optimal weight: 10.0000 chunk 2 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 41 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.176286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.128419 restraints weight = 3855.035| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.11 r_work: 0.3206 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3341 Z= 0.117 Angle : 0.477 5.324 4536 Z= 0.247 Chirality : 0.039 0.180 575 Planarity : 0.004 0.051 555 Dihedral : 3.270 13.595 455 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.22 % Allowed : 27.70 % Favored : 70.08 % 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: 2.09 (0.42), residues: 429 helix: 2.16 (0.30), residues: 320 sheet: 1.26 (1.52), residues: 18 loop : -1.50 (0.56), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 447 TYR 0.021 0.002 TYR A 305 PHE 0.009 0.001 PHE A 240 TRP 0.002 0.001 TRP A 276 HIS 0.001 0.001 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 3341) covalent geometry : angle 0.47696 ( 4536) hydrogen bonds : bond 0.04524 ( 229) hydrogen bonds : angle 3.89514 ( 681) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.125 Fit side-chains REVERT: A 200 TYR cc_start: 0.8126 (m-10) cc_final: 0.7736 (m-10) REVERT: A 231 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7221 (tp30) REVERT: A 428 LEU cc_start: 0.6719 (OUTLIER) cc_final: 0.6303 (mp) outliers start: 8 outliers final: 4 residues processed: 52 average time/residue: 0.4811 time to fit residues: 25.8567 Evaluate side-chains 49 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 35 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 30 optimal weight: 0.3980 chunk 10 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 3 optimal weight: 0.2980 chunk 33 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 41 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.178701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.129117 restraints weight = 3934.068| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.77 r_work: 0.3249 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3341 Z= 0.111 Angle : 0.467 5.113 4536 Z= 0.243 Chirality : 0.039 0.170 575 Planarity : 0.004 0.050 555 Dihedral : 3.287 13.925 455 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.77 % Allowed : 27.15 % Favored : 70.08 % 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: 2.09 (0.42), residues: 429 helix: 2.16 (0.30), residues: 320 sheet: 1.13 (1.47), residues: 18 loop : -1.48 (0.56), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 447 TYR 0.021 0.002 TYR A 305 PHE 0.011 0.001 PHE A 341 TRP 0.001 0.000 TRP A 19 HIS 0.001 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 3341) covalent geometry : angle 0.46705 ( 4536) hydrogen bonds : bond 0.04336 ( 229) hydrogen bonds : angle 3.85996 ( 681) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1405.32 seconds wall clock time: 24 minutes 37.32 seconds (1477.32 seconds total)