Starting phenix.real_space_refine on Wed Sep 17 03:41:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zng_60270/09_2025/8zng_60270.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zng_60270/09_2025/8zng_60270.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zng_60270/09_2025/8zng_60270.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zng_60270/09_2025/8zng_60270.map" model { file = "/net/cci-nas-00/data/ceres_data/8zng_60270/09_2025/8zng_60270.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zng_60270/09_2025/8zng_60270.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 14 5.16 5 C 2115 2.51 5 N 567 2.21 5 O 648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3347 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3273 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 416, 3262 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 395} Conformer: "B" Number of residues, atoms: 416, 3262 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 395} bond proxies already assigned to first conformer: 3322 Chain: "A" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 74 Unusual residues: {'AKG': 1, 'NDP': 1} Classifications: {'undetermined': 2, 'water': 16} Link IDs: {None: 17} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG A 187 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 187 " occ=0.50 Time building chain proxies: 1.82, per 1000 atoms: 0.54 Number of scatterers: 3347 At special positions: 0 Unit cell: (65.424, 63.168, 70.688, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 3 15.00 O 648 8.00 N 567 7.00 C 2115 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: 0.34 Conformation dependent library (CDL) restraints added in 293.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 760 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 3 sheets defined 55.5% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 5 through 18 Processing helix chain 'A' and resid 19 through 21 No H-bonds generated for 'chain 'A' and resid 19 through 21' Processing helix chain 'A' and resid 24 through 32 Processing helix chain 'A' and resid 79 through 97 removed outlier: 3.588A pdb=" N VAL A 97 " --> pdb=" O LYS A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 115 Processing helix chain 'A' and resid 116 through 132 Processing helix chain 'A' and resid 133 through 135 No H-bonds generated for 'chain 'A' and resid 133 through 135' Processing helix chain 'A' and resid 149 through 165 Processing helix chain 'A' and resid 170 through 174 removed outlier: 3.708A pdb=" N ILE A 174 " --> pdb=" O PHE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 206 Processing helix chain 'A' and resid 221 through 234 removed outlier: 3.800A pdb=" N TYR A 226 " --> pdb=" O ASN A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 280 through 286 removed outlier: 3.801A pdb=" N LEU A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 323 through 333 removed outlier: 3.975A pdb=" N ASP A 328 " --> pdb=" O PRO A 324 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE A 329 " --> pdb=" O GLU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 345 through 361 Processing helix chain 'A' and resid 365 through 391 Processing helix chain 'A' and resid 394 through 414 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 45 removed outlier: 6.683A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ARG A 73 " --> pdb=" O ILE A 108 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 45 removed outlier: 6.683A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N LYS A 69 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N GLY A 106 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N THR A 68 " --> pdb=" O ILE A 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 277 through 279 removed outlier: 7.626A pdb=" N VAL A 217 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL A 242 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU A 292 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL A 314 " --> pdb=" O ILE A 338 " (cutoff:3.500A) 195 hydrogen bonds defined for protein. 555 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: 0.56 Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1086 1.34 - 1.46: 617 1.46 - 1.58: 1672 1.58 - 1.69: 5 1.69 - 1.81: 27 Bond restraints: 3407 Sorted by residual: bond pdb=" O2B NDP A 500 " pdb=" P2B NDP A 500 " ideal model delta sigma weight residual 1.833 1.614 0.219 3.80e-02 6.93e+02 3.33e+01 bond pdb=" O5D NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 1.757 1.603 0.154 3.50e-02 8.16e+02 1.95e+01 bond pdb=" C2B NDP A 500 " pdb=" O2B NDP A 500 " ideal model delta sigma weight residual 1.330 1.423 -0.093 2.90e-02 1.19e+03 1.03e+01 bond pdb=" C5D NDP A 500 " pdb=" O5D NDP A 500 " ideal model delta sigma weight residual 1.368 1.448 -0.080 3.20e-02 9.77e+02 6.23e+00 bond pdb=" O2N NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 1.513 1.492 0.021 1.00e-02 1.00e+04 4.47e+00 ... (remaining 3402 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.67: 4598 4.67 - 9.34: 25 9.34 - 14.02: 1 14.02 - 18.69: 1 18.69 - 23.36: 1 Bond angle restraints: 4626 Sorted by residual: angle pdb=" PA NDP A 500 " pdb=" O3 NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 107.74 131.10 -23.36 1.95e+00 2.62e-01 1.43e+02 angle pdb=" C5B NDP A 500 " pdb=" O5B NDP A 500 " pdb=" PA NDP A 500 " ideal model delta sigma weight residual 103.84 117.90 -14.06 1.91e+00 2.73e-01 5.39e+01 angle pdb=" C5D NDP A 500 " pdb=" O5D NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 104.93 117.39 -12.46 2.66e+00 1.41e-01 2.20e+01 angle pdb=" O2N NDP A 500 " pdb=" PN NDP A 500 " pdb=" O5D NDP A 500 " ideal model delta sigma weight residual 100.52 109.31 -8.79 1.91e+00 2.74e-01 2.11e+01 angle pdb=" O1X NDP A 500 " pdb=" P2B NDP A 500 " pdb=" O3X NDP A 500 " ideal model delta sigma weight residual 117.46 112.22 5.24 1.17e+00 7.36e-01 2.02e+01 ... (remaining 4621 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 1929 36.00 - 71.99: 84 71.99 - 107.99: 8 107.99 - 143.98: 0 143.98 - 179.98: 1 Dihedral angle restraints: 2022 sinusoidal: 829 harmonic: 1193 Sorted by residual: dihedral pdb=" CD BARG A 187 " pdb=" NE BARG A 187 " pdb=" CZ BARG A 187 " pdb=" NH1BARG A 187 " ideal model delta sinusoidal sigma weight residual 0.00 179.98 -179.98 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" C5B NDP A 500 " pdb=" O5B NDP A 500 " pdb=" PA NDP A 500 " pdb=" O3 NDP A 500 " ideal model delta sinusoidal sigma weight residual 175.04 67.30 107.74 1 3.00e+01 1.11e-03 1.39e+01 dihedral pdb=" CA ASP A 307 " pdb=" CB ASP A 307 " pdb=" CG ASP A 307 " pdb=" OD1 ASP A 307 " ideal model delta sinusoidal sigma weight residual -30.00 -86.71 56.71 1 2.00e+01 2.50e-03 1.08e+01 ... (remaining 2019 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 390 0.050 - 0.100: 81 0.100 - 0.150: 27 0.150 - 0.200: 2 0.200 - 0.249: 2 Chirality restraints: 502 Sorted by residual: chirality pdb=" C4D NDP A 500 " pdb=" C3D NDP A 500 " pdb=" C5D NDP A 500 " pdb=" O4D NDP A 500 " both_signs ideal model delta sigma weight residual False -2.71 -2.46 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CB ILE A 4 " pdb=" CA ILE A 4 " pdb=" CG1 ILE A 4 " pdb=" CG2 ILE A 4 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" C1B NDP A 500 " pdb=" C2B NDP A 500 " pdb=" N9A NDP A 500 " pdb=" O4B NDP A 500 " both_signs ideal model delta sigma weight residual False 2.59 2.40 0.19 2.00e-01 2.50e+01 9.10e-01 ... (remaining 499 not shown) Planarity restraints: 592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2N NDP A 500 " 0.085 2.00e-02 2.50e+03 5.31e-02 3.52e+01 pdb=" C3N NDP A 500 " 0.015 2.00e-02 2.50e+03 pdb=" C4N NDP A 500 " 0.013 2.00e-02 2.50e+03 pdb=" C7N NDP A 500 " -0.046 2.00e-02 2.50e+03 pdb=" N1N NDP A 500 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 273 " -0.050 5.00e-02 4.00e+02 7.43e-02 8.84e+00 pdb=" N PRO A 274 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 274 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 274 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 149 " 0.031 5.00e-02 4.00e+02 4.68e-02 3.50e+00 pdb=" N PRO A 150 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 150 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 150 " 0.026 5.00e-02 4.00e+02 ... (remaining 589 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 1356 2.93 - 3.42: 3427 3.42 - 3.92: 6115 3.92 - 4.41: 6992 4.41 - 4.90: 11116 Nonbonded interactions: 29006 Sorted by model distance: nonbonded pdb=" OD1 ASP A 48 " pdb=" OG SER A 50 " model vdw 2.439 3.040 nonbonded pdb=" O LEU A 99 " pdb=" O HOH A 601 " model vdw 2.439 3.040 nonbonded pdb=" OE1 GLU A 354 " pdb=" O HOH A 602 " model vdw 2.481 3.040 nonbonded pdb=" NZ LYS A 177 " pdb=" OD1 ASN A 358 " model vdw 2.535 3.120 nonbonded pdb=" NE ARG A 65 " pdb=" O HOH A 601 " model vdw 2.549 3.120 ... (remaining 29001 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=0.50 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.450 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:6.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 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 0.219 3407 Z= 0.247 Angle : 0.920 23.360 4626 Z= 0.499 Chirality : 0.048 0.249 502 Planarity : 0.006 0.074 592 Dihedral : 19.319 179.977 1262 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.24 % Allowed : 17.94 % Favored : 78.82 % 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: 1.28 (0.43), residues: 417 helix: 2.31 (0.38), residues: 200 sheet: -0.02 (0.69), residues: 64 loop : -0.75 (0.48), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 165 TYR 0.012 0.001 TYR A 408 PHE 0.013 0.002 PHE A 381 TRP 0.010 0.001 TRP A 382 HIS 0.002 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00673 ( 3407) covalent geometry : angle 0.91992 ( 4626) hydrogen bonds : bond 0.13787 ( 180) hydrogen bonds : angle 5.80992 ( 555) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.155 Fit side-chains REVERT: A 388 HIS cc_start: 0.9048 (OUTLIER) cc_final: 0.8420 (p-80) outliers start: 10 outliers final: 6 residues processed: 75 average time/residue: 0.7486 time to fit residues: 57.3293 Evaluate side-chains 60 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 419 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 20.0000 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.107617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.078686 restraints weight = 10795.624| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 2.60 r_work: 0.2624 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2508 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2555 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2555 r_free = 0.2555 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2555 r_free = 0.2555 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2555 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9037 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3407 Z= 0.177 Angle : 0.553 7.613 4626 Z= 0.295 Chirality : 0.047 0.204 502 Planarity : 0.005 0.048 592 Dihedral : 11.739 179.770 485 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.35 % Allowed : 21.18 % Favored : 76.47 % 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: 1.03 (0.41), residues: 417 helix: 2.09 (0.36), residues: 203 sheet: 0.59 (0.79), residues: 54 loop : -1.20 (0.44), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 118 TYR 0.015 0.002 TYR A 363 PHE 0.013 0.002 PHE A 341 TRP 0.014 0.001 TRP A 382 HIS 0.004 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 3407) covalent geometry : angle 0.55349 ( 4626) hydrogen bonds : bond 0.05305 ( 180) hydrogen bonds : angle 4.33305 ( 555) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.130 Fit side-chains REVERT: A 210 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8446 (mp) REVERT: A 265 ARG cc_start: 0.7780 (ttp-170) cc_final: 0.7307 (ttm170) REVERT: A 286 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7594 (mp0) REVERT: A 304 LYS cc_start: 0.8343 (pttp) cc_final: 0.7936 (ptpt) outliers start: 7 outliers final: 2 residues processed: 62 average time/residue: 0.8195 time to fit residues: 51.9161 Evaluate side-chains 52 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 9.9990 chunk 3 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN A 267 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.110646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.082168 restraints weight = 11763.464| |-----------------------------------------------------------------------------| r_work (start): 0.2739 rms_B_bonded: 2.72 r_work: 0.2596 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2474 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2474 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2464 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2464 r_free = 0.2464 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2464 r_free = 0.2464 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2464 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9007 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3407 Z= 0.129 Angle : 0.487 6.672 4626 Z= 0.256 Chirality : 0.044 0.211 502 Planarity : 0.005 0.046 592 Dihedral : 10.969 179.739 474 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.35 % Allowed : 19.71 % Favored : 77.94 % 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: 1.02 (0.41), residues: 417 helix: 2.08 (0.36), residues: 204 sheet: 0.53 (0.79), residues: 56 loop : -1.21 (0.44), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 165 TYR 0.012 0.001 TYR A 363 PHE 0.013 0.001 PHE A 381 TRP 0.011 0.001 TRP A 382 HIS 0.003 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 3407) covalent geometry : angle 0.48658 ( 4626) hydrogen bonds : bond 0.04539 ( 180) hydrogen bonds : angle 4.17324 ( 555) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.138 Fit side-chains REVERT: A 210 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8576 (mp) REVERT: A 265 ARG cc_start: 0.7852 (ttp-170) cc_final: 0.7362 (ttm170) REVERT: A 286 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7598 (mp0) REVERT: A 290 ASP cc_start: 0.8597 (OUTLIER) cc_final: 0.8184 (t70) REVERT: A 304 LYS cc_start: 0.8313 (pttp) cc_final: 0.7922 (ptpt) outliers start: 7 outliers final: 2 residues processed: 54 average time/residue: 0.8401 time to fit residues: 46.3358 Evaluate side-chains 53 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 2 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 14 optimal weight: 0.0170 chunk 25 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.110329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.082022 restraints weight = 11642.709| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 2.68 r_work: 0.2607 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2486 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2486 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2534 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2534 r_free = 0.2534 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2534 r_free = 0.2534 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2534 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9004 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3407 Z= 0.121 Angle : 0.479 6.413 4626 Z= 0.251 Chirality : 0.044 0.218 502 Planarity : 0.004 0.046 592 Dihedral : 10.767 179.837 473 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.24 % Allowed : 19.12 % Favored : 77.65 % 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: 1.08 (0.41), residues: 417 helix: 2.12 (0.36), residues: 204 sheet: 0.60 (0.79), residues: 56 loop : -1.18 (0.44), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 118 TYR 0.011 0.001 TYR A 363 PHE 0.012 0.001 PHE A 381 TRP 0.011 0.001 TRP A 382 HIS 0.003 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 3407) covalent geometry : angle 0.47872 ( 4626) hydrogen bonds : bond 0.04339 ( 180) hydrogen bonds : angle 4.06491 ( 555) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.145 Fit side-chains REVERT: A 16 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.8481 (ttt90) REVERT: A 256 ASP cc_start: 0.8483 (t70) cc_final: 0.7927 (t70) REVERT: A 286 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7872 (mt-10) REVERT: A 290 ASP cc_start: 0.8569 (OUTLIER) cc_final: 0.8118 (t70) REVERT: A 304 LYS cc_start: 0.8274 (pttp) cc_final: 0.7910 (ptpt) outliers start: 10 outliers final: 5 residues processed: 55 average time/residue: 0.8112 time to fit residues: 45.5943 Evaluate side-chains 58 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 390 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 0.3980 chunk 34 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.112852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.085649 restraints weight = 14560.206| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 2.93 r_work: 0.2648 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2527 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2553 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2553 r_free = 0.2553 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2553 r_free = 0.2553 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2553 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8994 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3407 Z= 0.102 Angle : 0.456 5.937 4626 Z= 0.237 Chirality : 0.043 0.217 502 Planarity : 0.004 0.046 592 Dihedral : 10.284 179.934 471 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.35 % Allowed : 19.12 % Favored : 78.53 % 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: 1.20 (0.42), residues: 417 helix: 2.21 (0.36), residues: 204 sheet: 0.63 (0.78), residues: 56 loop : -1.11 (0.46), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 265 TYR 0.008 0.001 TYR A 363 PHE 0.010 0.001 PHE A 381 TRP 0.010 0.001 TRP A 382 HIS 0.003 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 3407) covalent geometry : angle 0.45628 ( 4626) hydrogen bonds : bond 0.03864 ( 180) hydrogen bonds : angle 3.94035 ( 555) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.150 Fit side-chains REVERT: A 8 GLU cc_start: 0.8779 (mt-10) cc_final: 0.7983 (pt0) REVERT: A 256 ASP cc_start: 0.8518 (t70) cc_final: 0.7934 (t70) REVERT: A 265 ARG cc_start: 0.7849 (ttp-170) cc_final: 0.7409 (mtt-85) REVERT: A 286 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7778 (mm-30) REVERT: A 290 ASP cc_start: 0.8576 (OUTLIER) cc_final: 0.8117 (t70) REVERT: A 304 LYS cc_start: 0.8240 (pttp) cc_final: 0.7895 (ptpt) outliers start: 7 outliers final: 3 residues processed: 54 average time/residue: 0.8198 time to fit residues: 45.2595 Evaluate side-chains 54 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 390 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 13 optimal weight: 0.3980 chunk 27 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 6 optimal weight: 0.8980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.110219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.082563 restraints weight = 9062.346| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 2.38 r_work: 0.2663 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2546 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2537 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2537 r_free = 0.2537 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2537 r_free = 0.2537 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2537 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3407 Z= 0.122 Angle : 0.480 6.121 4626 Z= 0.250 Chirality : 0.044 0.216 502 Planarity : 0.004 0.045 592 Dihedral : 10.192 179.872 471 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.06 % Allowed : 19.41 % Favored : 78.53 % 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: 1.18 (0.42), residues: 417 helix: 2.21 (0.36), residues: 204 sheet: 0.63 (0.78), residues: 56 loop : -1.13 (0.46), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 165 TYR 0.010 0.001 TYR A 363 PHE 0.011 0.001 PHE A 341 TRP 0.010 0.001 TRP A 382 HIS 0.003 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 3407) covalent geometry : angle 0.47994 ( 4626) hydrogen bonds : bond 0.04253 ( 180) hydrogen bonds : angle 3.99955 ( 555) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.154 Fit side-chains REVERT: A 256 ASP cc_start: 0.8516 (t70) cc_final: 0.7908 (t70) REVERT: A 265 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7399 (mtt-85) REVERT: A 290 ASP cc_start: 0.8494 (OUTLIER) cc_final: 0.8059 (t70) REVERT: A 304 LYS cc_start: 0.8218 (pttp) cc_final: 0.7867 (ptpt) outliers start: 6 outliers final: 3 residues processed: 54 average time/residue: 0.7903 time to fit residues: 43.6548 Evaluate side-chains 56 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 390 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 27 optimal weight: 0.0970 chunk 16 optimal weight: 4.9990 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.110116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.081405 restraints weight = 13756.104| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 2.91 r_work: 0.2588 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2468 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2468 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2469 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2469 r_free = 0.2469 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2469 r_free = 0.2469 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2469 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9016 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3407 Z= 0.129 Angle : 0.488 6.144 4626 Z= 0.255 Chirality : 0.044 0.214 502 Planarity : 0.004 0.046 592 Dihedral : 10.089 179.831 471 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.65 % Allowed : 18.82 % Favored : 78.53 % 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: 1.16 (0.42), residues: 417 helix: 2.18 (0.36), residues: 204 sheet: 0.66 (0.78), residues: 56 loop : -1.14 (0.46), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 165 TYR 0.011 0.001 TYR A 363 PHE 0.011 0.002 PHE A 381 TRP 0.010 0.001 TRP A 382 HIS 0.004 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 3407) covalent geometry : angle 0.48798 ( 4626) hydrogen bonds : bond 0.04361 ( 180) hydrogen bonds : angle 4.02940 ( 555) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.135 Fit side-chains REVERT: A 256 ASP cc_start: 0.8560 (t70) cc_final: 0.7945 (t70) REVERT: A 265 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7451 (mtt-85) REVERT: A 286 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7547 (mm-30) REVERT: A 290 ASP cc_start: 0.8579 (OUTLIER) cc_final: 0.8136 (t70) REVERT: A 304 LYS cc_start: 0.8218 (pttp) cc_final: 0.7865 (ptpt) outliers start: 8 outliers final: 3 residues processed: 55 average time/residue: 0.8030 time to fit residues: 45.1578 Evaluate side-chains 57 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 390 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 27 optimal weight: 0.0470 chunk 17 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 overall best weight: 1.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.109780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.081690 restraints weight = 10964.842| |-----------------------------------------------------------------------------| r_work (start): 0.2753 rms_B_bonded: 2.59 r_work: 0.2612 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2494 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2494 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2479 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2479 r_free = 0.2479 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2479 r_free = 0.2479 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2479 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9007 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3407 Z= 0.130 Angle : 0.492 6.135 4626 Z= 0.256 Chirality : 0.044 0.209 502 Planarity : 0.004 0.046 592 Dihedral : 9.997 179.854 471 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.06 % Allowed : 19.41 % Favored : 78.53 % 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: 1.17 (0.42), residues: 417 helix: 2.18 (0.36), residues: 204 sheet: 0.67 (0.78), residues: 56 loop : -1.12 (0.47), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 165 TYR 0.011 0.001 TYR A 363 PHE 0.012 0.002 PHE A 381 TRP 0.010 0.001 TRP A 382 HIS 0.004 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 3407) covalent geometry : angle 0.49219 ( 4626) hydrogen bonds : bond 0.04375 ( 180) hydrogen bonds : angle 4.04205 ( 555) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.128 Fit side-chains REVERT: A 256 ASP cc_start: 0.8562 (t70) cc_final: 0.7954 (t70) REVERT: A 265 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7447 (mtt-85) REVERT: A 286 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7632 (mm-30) REVERT: A 290 ASP cc_start: 0.8558 (OUTLIER) cc_final: 0.8132 (t70) REVERT: A 304 LYS cc_start: 0.8216 (pttp) cc_final: 0.7858 (ptpt) outliers start: 6 outliers final: 4 residues processed: 54 average time/residue: 0.7761 time to fit residues: 42.8228 Evaluate side-chains 58 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 390 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 29 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 14 optimal weight: 0.0070 chunk 5 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 30 optimal weight: 20.0000 chunk 25 optimal weight: 0.6980 overall best weight: 2.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.108238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.080058 restraints weight = 10865.590| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 2.58 r_work: 0.2601 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2481 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2481 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2446 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2446 r_free = 0.2446 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2446 r_free = 0.2446 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2446 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9023 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3407 Z= 0.152 Angle : 0.512 6.343 4626 Z= 0.268 Chirality : 0.045 0.209 502 Planarity : 0.004 0.046 592 Dihedral : 10.018 179.786 471 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.35 % Allowed : 19.12 % Favored : 78.53 % 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: 1.09 (0.42), residues: 417 helix: 2.10 (0.36), residues: 204 sheet: 0.67 (0.79), residues: 56 loop : -1.17 (0.47), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 165 TYR 0.013 0.001 TYR A 363 PHE 0.013 0.002 PHE A 381 TRP 0.011 0.001 TRP A 382 HIS 0.004 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 3407) covalent geometry : angle 0.51236 ( 4626) hydrogen bonds : bond 0.04736 ( 180) hydrogen bonds : angle 4.13335 ( 555) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.131 Fit side-chains REVERT: A 256 ASP cc_start: 0.8544 (t70) cc_final: 0.7955 (t70) REVERT: A 265 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7458 (mtt-85) REVERT: A 286 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7589 (mm-30) REVERT: A 290 ASP cc_start: 0.8581 (OUTLIER) cc_final: 0.8160 (t70) REVERT: A 304 LYS cc_start: 0.8262 (pttp) cc_final: 0.7894 (ptpt) outliers start: 7 outliers final: 4 residues processed: 55 average time/residue: 0.7528 time to fit residues: 42.3087 Evaluate side-chains 59 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 390 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 19 optimal weight: 2.9990 chunk 13 optimal weight: 0.2980 chunk 27 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 17 optimal weight: 0.0870 chunk 14 optimal weight: 0.0670 overall best weight: 0.6900 ------------------------------------------------------------------------------- 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 = 0.3248 r_free = 0.3248 target = 0.112972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.085929 restraints weight = 8399.042| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 2.29 r_work: 0.2703 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2585 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2552 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2552 r_free = 0.2552 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2552 r_free = 0.2552 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2552 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3407 Z= 0.100 Angle : 0.465 5.716 4626 Z= 0.241 Chirality : 0.042 0.206 502 Planarity : 0.004 0.047 592 Dihedral : 9.848 179.997 471 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.76 % Allowed : 19.41 % Favored : 78.82 % 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: 1.26 (0.42), residues: 417 helix: 2.24 (0.36), residues: 204 sheet: 0.66 (0.78), residues: 56 loop : -1.05 (0.47), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 165 TYR 0.008 0.001 TYR A 363 PHE 0.009 0.001 PHE A 381 TRP 0.008 0.001 TRP A 382 HIS 0.002 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 3407) covalent geometry : angle 0.46533 ( 4626) hydrogen bonds : bond 0.03746 ( 180) hydrogen bonds : angle 3.91904 ( 555) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.103 Fit side-chains REVERT: A 8 GLU cc_start: 0.8703 (mt-10) cc_final: 0.7932 (pt0) REVERT: A 256 ASP cc_start: 0.8525 (t70) cc_final: 0.7931 (t70) REVERT: A 265 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7452 (mtt-85) REVERT: A 290 ASP cc_start: 0.8492 (OUTLIER) cc_final: 0.8050 (t70) REVERT: A 304 LYS cc_start: 0.8198 (pttp) cc_final: 0.7869 (ptpt) outliers start: 5 outliers final: 3 residues processed: 53 average time/residue: 0.8082 time to fit residues: 43.7571 Evaluate side-chains 57 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 390 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 37 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 17 optimal weight: 0.0570 chunk 38 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 overall best weight: 2.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.108037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.079083 restraints weight = 14338.887| |-----------------------------------------------------------------------------| r_work (start): 0.2702 rms_B_bonded: 2.93 r_work: 0.2549 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2429 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2429 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2481 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2481 r_free = 0.2481 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2481 r_free = 0.2481 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2481 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9043 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3407 Z= 0.175 Angle : 0.541 7.016 4626 Z= 0.282 Chirality : 0.046 0.208 502 Planarity : 0.005 0.046 592 Dihedral : 10.020 179.729 471 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.06 % Allowed : 19.41 % Favored : 78.53 % 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: 1.07 (0.42), residues: 417 helix: 2.06 (0.36), residues: 204 sheet: 0.63 (0.78), residues: 56 loop : -1.11 (0.47), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 118 TYR 0.014 0.002 TYR A 363 PHE 0.014 0.002 PHE A 341 TRP 0.012 0.001 TRP A 382 HIS 0.005 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 3407) covalent geometry : angle 0.54148 ( 4626) hydrogen bonds : bond 0.04951 ( 180) hydrogen bonds : angle 4.16074 ( 555) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1766.85 seconds wall clock time: 30 minutes 58.21 seconds (1858.21 seconds total)