Starting phenix.real_space_refine on Fri Aug 22 13:14:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z7w_39830/08_2025/8z7w_39830.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z7w_39830/08_2025/8z7w_39830.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8z7w_39830/08_2025/8z7w_39830.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z7w_39830/08_2025/8z7w_39830.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8z7w_39830/08_2025/8z7w_39830.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z7w_39830/08_2025/8z7w_39830.map" } resolution = 3.09 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= 0.103 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 15 5.16 5 C 2095 2.51 5 N 468 2.21 5 O 529 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3107 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3098 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 13, 'TRANS': 373} Chain breaks: 1 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'MF8': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.97, per 1000 atoms: 0.31 Number of scatterers: 3107 At special positions: 0 Unit cell: (64, 68, 71, 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 15 16.00 O 529 8.00 N 468 7.00 C 2095 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: 0.27 Conformation dependent library (CDL) restraints added in 112.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 734 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 0 sheets defined 87.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 12 through 28 Processing helix chain 'A' and resid 32 through 36 removed outlier: 3.553A pdb=" N LEU A 35 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ILE A 36 " --> pdb=" O PRO A 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 32 through 36' Processing helix chain 'A' and resid 37 through 41 removed outlier: 3.729A pdb=" N SER A 40 " --> pdb=" O PRO A 37 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY A 41 " --> pdb=" O TYR A 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 37 through 41' Processing helix chain 'A' and resid 48 through 53 removed outlier: 3.626A pdb=" N THR A 52 " --> pdb=" O SER A 48 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN A 53 " --> pdb=" O ALA A 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 48 through 53' Processing helix chain 'A' and resid 55 through 73 removed outlier: 4.019A pdb=" N TRP A 59 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N THR A 60 " --> pdb=" O PHE A 56 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR A 61 " --> pdb=" O PRO A 57 " (cutoff:3.500A) Proline residue: A 69 - end of helix removed outlier: 3.864A pdb=" N VAL A 72 " --> pdb=" O LEU A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 99 removed outlier: 3.590A pdb=" N ILE A 83 " --> pdb=" O TYR A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 131 removed outlier: 3.502A pdb=" N MET A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE A 127 " --> pdb=" O TYR A 123 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N TYR A 128 " --> pdb=" O TYR A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 135 through 164 Processing helix chain 'A' and resid 168 through 189 Processing helix chain 'A' and resid 262 through 274 Processing helix chain 'A' and resid 280 through 307 removed outlier: 4.286A pdb=" N ALA A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY A 291 " --> pdb=" O PHE A 287 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N GLN A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ILE A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 337 removed outlier: 4.446A pdb=" N GLY A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA A 318 " --> pdb=" O ILE A 314 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA A 323 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 366 removed outlier: 3.720A pdb=" N LEU A 344 " --> pdb=" O ASN A 340 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N GLU A 346 " --> pdb=" O ASP A 342 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 398 Processing helix chain 'A' and resid 402 through 426 Processing helix chain 'A' and resid 434 through 461 removed outlier: 3.913A pdb=" N PHE A 439 " --> pdb=" O VAL A 435 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LEU A 440 " --> pdb=" O SER A 436 " (cutoff:3.500A) 240 hydrogen bonds defined for protein. 720 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: 0.48 Time building geometry restraints manager: 0.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 449 1.30 - 1.43: 966 1.43 - 1.56: 1758 1.56 - 1.69: 0 1.69 - 1.82: 26 Bond restraints: 3199 Sorted by residual: bond pdb=" C ALA A 447 " pdb=" O ALA A 447 " ideal model delta sigma weight residual 1.236 1.164 0.072 1.18e-02 7.18e+03 3.75e+01 bond pdb=" C ALA A 450 " pdb=" O ALA A 450 " ideal model delta sigma weight residual 1.237 1.166 0.071 1.17e-02 7.31e+03 3.66e+01 bond pdb=" C PRO A 69 " pdb=" O PRO A 69 " ideal model delta sigma weight residual 1.235 1.174 0.061 1.30e-02 5.92e+03 2.18e+01 bond pdb=" C ALA A 321 " pdb=" O ALA A 321 " ideal model delta sigma weight residual 1.236 1.180 0.056 1.22e-02 6.72e+03 2.14e+01 bond pdb=" C TYR A 315 " pdb=" O TYR A 315 " ideal model delta sigma weight residual 1.234 1.186 0.048 1.17e-02 7.31e+03 1.72e+01 ... (remaining 3194 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 4159 2.21 - 4.41: 173 4.41 - 6.62: 29 6.62 - 8.83: 6 8.83 - 11.04: 5 Bond angle restraints: 4372 Sorted by residual: angle pdb=" N LEU A 35 " pdb=" CA LEU A 35 " pdb=" C LEU A 35 " ideal model delta sigma weight residual 112.04 102.68 9.36 1.44e+00 4.82e-01 4.23e+01 angle pdb=" N ALA A 447 " pdb=" CA ALA A 447 " pdb=" C ALA A 447 " ideal model delta sigma weight residual 111.33 104.22 7.11 1.21e+00 6.83e-01 3.46e+01 angle pdb=" CB GLU A 320 " pdb=" CG GLU A 320 " pdb=" CD GLU A 320 " ideal model delta sigma weight residual 112.60 122.33 -9.73 1.70e+00 3.46e-01 3.27e+01 angle pdb=" C ASN A 45 " pdb=" CA ASN A 45 " pdb=" CB ASN A 45 " ideal model delta sigma weight residual 111.80 119.94 -8.14 1.46e+00 4.69e-01 3.11e+01 angle pdb=" C THR A 47 " pdb=" CA THR A 47 " pdb=" CB THR A 47 " ideal model delta sigma weight residual 109.76 120.80 -11.04 1.99e+00 2.53e-01 3.08e+01 ... (remaining 4367 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.33: 1504 16.33 - 32.67: 222 32.67 - 49.00: 59 49.00 - 65.33: 20 65.33 - 81.66: 3 Dihedral angle restraints: 1808 sinusoidal: 659 harmonic: 1149 Sorted by residual: dihedral pdb=" C ASN A 45 " pdb=" N ASN A 45 " pdb=" CA ASN A 45 " pdb=" CB ASN A 45 " ideal model delta harmonic sigma weight residual -122.60 -142.73 20.13 0 2.50e+00 1.60e-01 6.48e+01 dihedral pdb=" N ASN A 45 " pdb=" C ASN A 45 " pdb=" CA ASN A 45 " pdb=" CB ASN A 45 " ideal model delta harmonic sigma weight residual 122.80 141.30 -18.50 0 2.50e+00 1.60e-01 5.48e+01 dihedral pdb=" C THR A 47 " pdb=" N THR A 47 " pdb=" CA THR A 47 " pdb=" CB THR A 47 " ideal model delta harmonic sigma weight residual -122.00 -133.88 11.88 0 2.50e+00 1.60e-01 2.26e+01 ... (remaining 1805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.151: 484 0.151 - 0.301: 18 0.301 - 0.452: 2 0.452 - 0.603: 0 0.603 - 0.753: 1 Chirality restraints: 505 Sorted by residual: chirality pdb=" CA ASN A 45 " pdb=" N ASN A 45 " pdb=" C ASN A 45 " pdb=" CB ASN A 45 " both_signs ideal model delta sigma weight residual False 2.51 1.76 0.75 2.00e-01 2.50e+01 1.42e+01 chirality pdb=" CA LEU A 46 " pdb=" N LEU A 46 " pdb=" C LEU A 46 " pdb=" CB LEU A 46 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CA ILE A 449 " pdb=" N ILE A 449 " pdb=" C ILE A 449 " pdb=" CB ILE A 449 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.33e+00 ... (remaining 502 not shown) Planarity restraints: 524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C01 MF8 A 501 " -0.438 2.00e-02 2.50e+03 3.18e-01 2.27e+03 pdb=" C03 MF8 A 501 " 0.491 2.00e-02 2.50e+03 pdb=" C04 MF8 A 501 " -0.007 2.00e-02 2.50e+03 pdb=" C07 MF8 A 501 " -0.015 2.00e-02 2.50e+03 pdb=" N02 MF8 A 501 " 0.013 2.00e-02 2.50e+03 pdb=" N05 MF8 A 501 " -0.000 2.00e-02 2.50e+03 pdb=" N06 MF8 A 501 " -0.032 2.00e-02 2.50e+03 pdb=" N08 MF8 A 501 " -0.492 2.00e-02 2.50e+03 pdb=" N09 MF8 A 501 " 0.481 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 69 " -0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C PRO A 69 " 0.056 2.00e-02 2.50e+03 pdb=" O PRO A 69 " -0.022 2.00e-02 2.50e+03 pdb=" N VAL A 70 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 70 " 0.014 2.00e-02 2.50e+03 2.77e-02 7.69e+00 pdb=" C VAL A 70 " -0.048 2.00e-02 2.50e+03 pdb=" O VAL A 70 " 0.017 2.00e-02 2.50e+03 pdb=" N PHE A 71 " 0.017 2.00e-02 2.50e+03 ... (remaining 521 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 699 2.77 - 3.30: 3279 3.30 - 3.84: 5570 3.84 - 4.37: 6550 4.37 - 4.90: 11132 Nonbonded interactions: 27230 Sorted by model distance: nonbonded pdb=" OD1 ASP A 75 " pdb=" OH TYR A 79 " model vdw 2.241 3.040 nonbonded pdb=" OE1 GLN A 294 " pdb=" OH TYR A 442 " model vdw 2.247 3.040 nonbonded pdb=" OH TYR A 128 " pdb=" OG SER A 140 " model vdw 2.257 3.040 nonbonded pdb=" O PHE A 287 " pdb=" OH TYR A 445 " model vdw 2.319 3.040 nonbonded pdb=" OH TYR A 126 " pdb=" O PRO A 191 " model vdw 2.325 3.040 ... (remaining 27225 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: 1.050 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: 0.010 Extract box with map and model: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.870 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 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 : 0.007 0.072 3199 Z= 0.480 Angle : 1.027 11.035 4372 Z= 0.687 Chirality : 0.070 0.753 505 Planarity : 0.015 0.318 524 Dihedral : 17.007 81.664 1074 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 20.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.30 % Allowed : 25.83 % Favored : 70.87 % Cbeta Deviations : 0.82 % 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 aren not related in a simple way. whole: -0.06 (0.43), residues: 383 helix: 0.09 (0.28), residues: 318 sheet: None (None), residues: 0 loop : 0.09 (0.88), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 456 TYR 0.017 0.002 TYR A 459 PHE 0.031 0.002 PHE A 279 TRP 0.014 0.001 TRP A 94 HIS 0.002 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00694 ( 3199) covalent geometry : angle 1.02651 ( 4372) hydrogen bonds : bond 0.17224 ( 240) hydrogen bonds : angle 7.51358 ( 720) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.085 Fit side-chains REVERT: A 280 TYR cc_start: 0.8306 (t80) cc_final: 0.7886 (t80) REVERT: A 340 ASN cc_start: 0.8034 (p0) cc_final: 0.7305 (t0) outliers start: 11 outliers final: 4 residues processed: 52 average time/residue: 0.0667 time to fit residues: 4.1641 Evaluate side-chains 45 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 454 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.133302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.113617 restraints weight = 3752.042| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.58 r_work: 0.3116 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3199 Z= 0.185 Angle : 0.662 8.999 4372 Z= 0.346 Chirality : 0.044 0.210 505 Planarity : 0.005 0.036 524 Dihedral : 5.066 31.602 429 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.30 % Allowed : 24.62 % Favored : 72.07 % 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 aren not related in a simple way. whole: 1.19 (0.43), residues: 383 helix: 0.95 (0.29), residues: 325 sheet: None (None), residues: 0 loop : 0.46 (0.89), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 456 TYR 0.014 0.002 TYR A 280 PHE 0.020 0.002 PHE A 71 TRP 0.018 0.002 TRP A 94 HIS 0.004 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 3199) covalent geometry : angle 0.66237 ( 4372) hydrogen bonds : bond 0.05659 ( 240) hydrogen bonds : angle 4.72107 ( 720) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.128 Fit side-chains REVERT: A 120 GLU cc_start: 0.6820 (OUTLIER) cc_final: 0.6384 (pt0) REVERT: A 265 TRP cc_start: 0.7969 (t60) cc_final: 0.7623 (t60) REVERT: A 315 TYR cc_start: 0.7913 (OUTLIER) cc_final: 0.6889 (t80) REVERT: A 340 ASN cc_start: 0.8169 (p0) cc_final: 0.7112 (t0) REVERT: A 385 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8131 (tp) outliers start: 11 outliers final: 5 residues processed: 57 average time/residue: 0.0469 time to fit residues: 3.6233 Evaluate side-chains 50 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 426 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 8 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.151465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.130706 restraints weight = 3527.665| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.68 r_work: 0.3413 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3199 Z= 0.171 Angle : 0.619 9.650 4372 Z= 0.320 Chirality : 0.043 0.214 505 Planarity : 0.004 0.035 524 Dihedral : 4.375 19.727 423 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 4.20 % Allowed : 24.02 % Favored : 71.77 % 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 aren not related in a simple way. whole: 1.39 (0.43), residues: 383 helix: 1.10 (0.28), residues: 327 sheet: None (None), residues: 0 loop : 0.36 (0.90), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 277 TYR 0.013 0.002 TYR A 298 PHE 0.016 0.001 PHE A 71 TRP 0.018 0.002 TRP A 94 HIS 0.003 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 3199) covalent geometry : angle 0.61886 ( 4372) hydrogen bonds : bond 0.05193 ( 240) hydrogen bonds : angle 4.39192 ( 720) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.157 Fit side-chains REVERT: A 120 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6759 (pt0) REVERT: A 146 VAL cc_start: 0.8668 (OUTLIER) cc_final: 0.8425 (t) REVERT: A 265 TRP cc_start: 0.8260 (t60) cc_final: 0.7912 (t60) REVERT: A 280 TYR cc_start: 0.8142 (OUTLIER) cc_final: 0.6425 (m-80) REVERT: A 315 TYR cc_start: 0.8033 (OUTLIER) cc_final: 0.6979 (t80) REVERT: A 340 ASN cc_start: 0.8339 (p0) cc_final: 0.7213 (t0) REVERT: A 385 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8273 (tp) REVERT: A 438 GLN cc_start: 0.7235 (OUTLIER) cc_final: 0.7028 (tt0) outliers start: 14 outliers final: 8 residues processed: 53 average time/residue: 0.0349 time to fit residues: 2.6130 Evaluate side-chains 56 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 438 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 12 optimal weight: 0.0070 chunk 28 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.153375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.132664 restraints weight = 3545.789| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.69 r_work: 0.3410 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3199 Z= 0.151 Angle : 0.588 9.825 4372 Z= 0.304 Chirality : 0.042 0.207 505 Planarity : 0.004 0.034 524 Dihedral : 4.263 19.854 423 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 6.61 % Allowed : 22.22 % Favored : 71.17 % 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 aren not related in a simple way. whole: 1.60 (0.43), residues: 383 helix: 1.26 (0.29), residues: 324 sheet: None (None), residues: 0 loop : 0.38 (0.92), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 277 TYR 0.012 0.001 TYR A 38 PHE 0.014 0.001 PHE A 71 TRP 0.017 0.001 TRP A 94 HIS 0.004 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 3199) covalent geometry : angle 0.58820 ( 4372) hydrogen bonds : bond 0.04902 ( 240) hydrogen bonds : angle 4.27907 ( 720) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 44 time to evaluate : 0.065 Fit side-chains revert: symmetry clash REVERT: A 120 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6762 (pt0) REVERT: A 146 VAL cc_start: 0.8726 (OUTLIER) cc_final: 0.8498 (t) REVERT: A 265 TRP cc_start: 0.8349 (t60) cc_final: 0.8043 (t60) REVERT: A 280 TYR cc_start: 0.8215 (OUTLIER) cc_final: 0.6569 (m-80) REVERT: A 340 ASN cc_start: 0.8369 (p0) cc_final: 0.7308 (t0) REVERT: A 385 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8275 (tp) REVERT: A 452 ILE cc_start: 0.7626 (mt) cc_final: 0.7254 (mt) outliers start: 22 outliers final: 10 residues processed: 61 average time/residue: 0.0381 time to fit residues: 3.0890 Evaluate side-chains 52 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 38 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 437 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 17 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 12 optimal weight: 0.0870 chunk 26 optimal weight: 0.9980 chunk 8 optimal weight: 0.3980 chunk 18 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.153310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.132847 restraints weight = 3500.792| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.67 r_work: 0.3413 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3199 Z= 0.151 Angle : 0.581 10.003 4372 Z= 0.299 Chirality : 0.042 0.200 505 Planarity : 0.004 0.035 524 Dihedral : 4.248 20.199 423 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 6.31 % Allowed : 20.42 % Favored : 73.27 % 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 aren not related in a simple way. whole: 1.58 (0.43), residues: 383 helix: 1.26 (0.29), residues: 323 sheet: None (None), residues: 0 loop : 0.30 (0.89), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 138 TYR 0.012 0.001 TYR A 280 PHE 0.014 0.001 PHE A 71 TRP 0.017 0.001 TRP A 94 HIS 0.003 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 3199) covalent geometry : angle 0.58111 ( 4372) hydrogen bonds : bond 0.04763 ( 240) hydrogen bonds : angle 4.23329 ( 720) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 43 time to evaluate : 0.077 Fit side-chains revert: symmetry clash REVERT: A 120 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6740 (pt0) REVERT: A 146 VAL cc_start: 0.8748 (OUTLIER) cc_final: 0.8485 (t) REVERT: A 265 TRP cc_start: 0.8391 (t60) cc_final: 0.8120 (t60) REVERT: A 280 TYR cc_start: 0.8207 (OUTLIER) cc_final: 0.6585 (m-80) REVERT: A 340 ASN cc_start: 0.8309 (p0) cc_final: 0.7306 (t0) REVERT: A 385 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8261 (tp) outliers start: 21 outliers final: 12 residues processed: 59 average time/residue: 0.0317 time to fit residues: 2.5275 Evaluate side-chains 55 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 39 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 437 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 24 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 0.0020 chunk 10 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.153133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.132634 restraints weight = 3524.872| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.67 r_work: 0.3412 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3199 Z= 0.153 Angle : 0.579 9.948 4372 Z= 0.298 Chirality : 0.042 0.204 505 Planarity : 0.004 0.035 524 Dihedral : 4.227 20.124 423 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 5.41 % Allowed : 20.12 % Favored : 74.47 % 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 aren not related in a simple way. whole: 1.71 (0.43), residues: 383 helix: 1.38 (0.29), residues: 321 sheet: None (None), residues: 0 loop : 0.14 (0.85), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 138 TYR 0.012 0.001 TYR A 298 PHE 0.014 0.001 PHE A 71 TRP 0.017 0.001 TRP A 94 HIS 0.004 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 3199) covalent geometry : angle 0.57923 ( 4372) hydrogen bonds : bond 0.04717 ( 240) hydrogen bonds : angle 4.18329 ( 720) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 46 time to evaluate : 0.102 Fit side-chains revert: symmetry clash REVERT: A 120 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6911 (pt0) REVERT: A 146 VAL cc_start: 0.8755 (OUTLIER) cc_final: 0.8490 (t) REVERT: A 265 TRP cc_start: 0.8382 (t60) cc_final: 0.8153 (t60) REVERT: A 280 TYR cc_start: 0.8192 (OUTLIER) cc_final: 0.6541 (m-80) REVERT: A 340 ASN cc_start: 0.8363 (p0) cc_final: 0.7261 (t0) REVERT: A 385 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8280 (tp) outliers start: 18 outliers final: 13 residues processed: 58 average time/residue: 0.0340 time to fit residues: 2.6635 Evaluate side-chains 58 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 41 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 437 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 36 optimal weight: 0.0980 chunk 24 optimal weight: 0.9990 chunk 12 optimal weight: 0.0170 chunk 2 optimal weight: 0.8980 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.154267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.133885 restraints weight = 3528.403| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.67 r_work: 0.3410 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3199 Z= 0.144 Angle : 0.585 9.911 4372 Z= 0.297 Chirality : 0.041 0.200 505 Planarity : 0.004 0.035 524 Dihedral : 4.204 20.289 423 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 5.71 % Allowed : 20.42 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.43), residues: 383 helix: 1.44 (0.29), residues: 321 sheet: None (None), residues: 0 loop : 0.14 (0.85), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 277 TYR 0.013 0.001 TYR A 383 PHE 0.013 0.001 PHE A 71 TRP 0.017 0.001 TRP A 94 HIS 0.004 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 3199) covalent geometry : angle 0.58538 ( 4372) hydrogen bonds : bond 0.04616 ( 240) hydrogen bonds : angle 4.14381 ( 720) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 42 time to evaluate : 0.116 Fit side-chains revert: symmetry clash REVERT: A 120 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6994 (pt0) REVERT: A 146 VAL cc_start: 0.8750 (OUTLIER) cc_final: 0.8490 (t) REVERT: A 265 TRP cc_start: 0.8354 (t60) cc_final: 0.8117 (t60) REVERT: A 280 TYR cc_start: 0.8241 (OUTLIER) cc_final: 0.6557 (m-80) REVERT: A 340 ASN cc_start: 0.8366 (p0) cc_final: 0.7268 (t0) REVERT: A 385 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8275 (tp) outliers start: 19 outliers final: 12 residues processed: 55 average time/residue: 0.0417 time to fit residues: 3.1374 Evaluate side-chains 58 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 42 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 437 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 11 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 2 optimal weight: 0.0000 chunk 5 optimal weight: 0.7980 chunk 20 optimal weight: 0.3980 chunk 30 optimal weight: 0.6980 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.154720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.134381 restraints weight = 3542.659| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.67 r_work: 0.3428 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3199 Z= 0.142 Angle : 0.580 9.974 4372 Z= 0.294 Chirality : 0.041 0.196 505 Planarity : 0.004 0.035 524 Dihedral : 4.138 20.165 423 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 5.11 % Allowed : 20.72 % Favored : 74.17 % 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 aren not related in a simple way. whole: 1.86 (0.43), residues: 383 helix: 1.49 (0.29), residues: 321 sheet: None (None), residues: 0 loop : 0.20 (0.85), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 277 TYR 0.012 0.001 TYR A 383 PHE 0.014 0.001 PHE A 71 TRP 0.017 0.001 TRP A 94 HIS 0.004 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 3199) covalent geometry : angle 0.57951 ( 4372) hydrogen bonds : bond 0.04549 ( 240) hydrogen bonds : angle 4.10620 ( 720) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 47 time to evaluate : 0.081 Fit side-chains revert: symmetry clash REVERT: A 120 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6974 (pt0) REVERT: A 146 VAL cc_start: 0.8741 (OUTLIER) cc_final: 0.8485 (t) REVERT: A 265 TRP cc_start: 0.8390 (t60) cc_final: 0.8147 (t60) REVERT: A 280 TYR cc_start: 0.8220 (OUTLIER) cc_final: 0.6554 (m-80) REVERT: A 340 ASN cc_start: 0.8372 (p0) cc_final: 0.7278 (t0) REVERT: A 385 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8274 (tp) outliers start: 17 outliers final: 12 residues processed: 59 average time/residue: 0.0459 time to fit residues: 3.6095 Evaluate side-chains 60 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 437 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 25 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 10 optimal weight: 0.0970 chunk 34 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 8 optimal weight: 0.2980 chunk 4 optimal weight: 0.0470 chunk 26 optimal weight: 0.8980 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.155826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.135639 restraints weight = 3517.603| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.66 r_work: 0.3443 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3199 Z= 0.134 Angle : 0.569 9.853 4372 Z= 0.289 Chirality : 0.041 0.190 505 Planarity : 0.004 0.036 524 Dihedral : 4.096 20.291 423 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.50 % Allowed : 22.52 % Favored : 72.97 % 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 aren not related in a simple way. whole: 1.92 (0.43), residues: 383 helix: 1.55 (0.28), residues: 318 sheet: None (None), residues: 0 loop : 0.13 (0.85), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 277 TYR 0.019 0.001 TYR A 383 PHE 0.012 0.001 PHE A 71 TRP 0.017 0.001 TRP A 94 HIS 0.004 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 3199) covalent geometry : angle 0.56877 ( 4372) hydrogen bonds : bond 0.04474 ( 240) hydrogen bonds : angle 4.07741 ( 720) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.110 Fit side-chains revert: symmetry clash REVERT: A 120 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6946 (pt0) REVERT: A 146 VAL cc_start: 0.8725 (OUTLIER) cc_final: 0.8462 (t) REVERT: A 265 TRP cc_start: 0.8392 (t60) cc_final: 0.8147 (t60) REVERT: A 280 TYR cc_start: 0.8216 (OUTLIER) cc_final: 0.6554 (m-80) REVERT: A 340 ASN cc_start: 0.8369 (p0) cc_final: 0.7292 (t0) REVERT: A 385 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8287 (tp) outliers start: 15 outliers final: 11 residues processed: 58 average time/residue: 0.0442 time to fit residues: 3.4757 Evaluate side-chains 60 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 437 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 12 optimal weight: 0.1980 chunk 25 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 8 optimal weight: 0.2980 chunk 36 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.152022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.132541 restraints weight = 3531.539| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.55 r_work: 0.3447 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3199 Z= 0.145 Angle : 0.581 9.901 4372 Z= 0.295 Chirality : 0.041 0.192 505 Planarity : 0.004 0.038 524 Dihedral : 4.117 20.034 423 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.80 % Allowed : 22.52 % Favored : 72.67 % 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 aren not related in a simple way. whole: 1.91 (0.43), residues: 383 helix: 1.51 (0.28), residues: 322 sheet: None (None), residues: 0 loop : 0.29 (0.85), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 429 TYR 0.022 0.002 TYR A 383 PHE 0.014 0.001 PHE A 71 TRP 0.017 0.001 TRP A 94 HIS 0.004 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 3199) covalent geometry : angle 0.58063 ( 4372) hydrogen bonds : bond 0.04553 ( 240) hydrogen bonds : angle 4.10735 ( 720) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 46 time to evaluate : 0.114 Fit side-chains revert: symmetry clash REVERT: A 120 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6967 (pt0) REVERT: A 146 VAL cc_start: 0.8744 (OUTLIER) cc_final: 0.8469 (t) REVERT: A 265 TRP cc_start: 0.8421 (t60) cc_final: 0.8146 (t60) REVERT: A 280 TYR cc_start: 0.8206 (OUTLIER) cc_final: 0.6549 (m-80) REVERT: A 340 ASN cc_start: 0.8368 (p0) cc_final: 0.7300 (t0) REVERT: A 385 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8277 (tp) outliers start: 16 outliers final: 11 residues processed: 57 average time/residue: 0.0450 time to fit residues: 3.4976 Evaluate side-chains 60 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 437 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 27 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 20 optimal weight: 0.0070 chunk 22 optimal weight: 0.9980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.153141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.132561 restraints weight = 3603.594| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.69 r_work: 0.3407 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3199 Z= 0.158 Angle : 0.592 10.044 4372 Z= 0.300 Chirality : 0.042 0.200 505 Planarity : 0.004 0.038 524 Dihedral : 4.177 20.150 423 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.20 % Allowed : 23.12 % Favored : 72.67 % 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 aren not related in a simple way. whole: 1.93 (0.43), residues: 383 helix: 1.46 (0.28), residues: 323 sheet: None (None), residues: 0 loop : 0.68 (0.86), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 144 TYR 0.020 0.002 TYR A 383 PHE 0.014 0.001 PHE A 71 TRP 0.017 0.001 TRP A 94 HIS 0.004 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 3199) covalent geometry : angle 0.59219 ( 4372) hydrogen bonds : bond 0.04660 ( 240) hydrogen bonds : angle 4.15464 ( 720) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 901.96 seconds wall clock time: 16 minutes 12.02 seconds (972.02 seconds total)