Starting phenix.real_space_refine on Wed Sep 17 03:42:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8znc_60267/09_2025/8znc_60267.cif Found real_map, /net/cci-nas-00/data/ceres_data/8znc_60267/09_2025/8znc_60267.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8znc_60267/09_2025/8znc_60267.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8znc_60267/09_2025/8znc_60267.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8znc_60267/09_2025/8znc_60267.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8znc_60267/09_2025/8znc_60267.map" } resolution = 2.41 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 2118 2.51 5 N 565 2.21 5 O 656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 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: 3356 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: 3321 Chain: "A" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 83 Unusual residues: {'AKG': 1, 'NDP': 1, 'NH4': 1} Classifications: {'undetermined': 3, 'water': 24} Link IDs: {None: 26} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE A 89 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 89 " occ=0.50 Time building chain proxies: 1.56, per 1000 atoms: 0.46 Number of scatterers: 3356 At special positions: 0 Unit cell: (66.176, 63.92, 72.192, 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 656 8.00 N 565 7.00 C 2118 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: 0.36 Conformation dependent library (CDL) restraints added in 205.9 milliseconds Enol-peptide restraints added in 238.4 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: 18 helices and 2 sheets defined 56.0% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 5 through 19 removed outlier: 3.933A pdb=" N GLN A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 32 Processing helix chain 'A' and resid 79 through 97 removed outlier: 3.692A 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 169 through 174 removed outlier: 3.583A pdb=" N GLY A 172 " --> pdb=" O PRO A 169 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE A 174 " --> pdb=" O PHE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 207 Processing helix chain 'A' and resid 221 through 234 removed outlier: 3.741A 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 Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 323 through 334 removed outlier: 3.532A pdb=" N GLU A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS A 333 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY A 334 " --> pdb=" O LEU A 330 " (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 392 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: 4.663A pdb=" N THR A 55 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N LYS A 69 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N GLY A 106 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N GLY A 71 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ILE A 108 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ARG A 73 " --> pdb=" O ILE A 108 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR A 68 " --> pdb=" O ILE A 141 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ALA A 143 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N GLY A 70 " --> pdb=" O ALA A 143 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 277 through 279 removed outlier: 3.536A pdb=" N THR A 277 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ILE A 215 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N VAL A 242 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL A 217 " --> pdb=" O VAL A 242 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA A 293 " --> pdb=" O ALA A 216 " (cutoff:3.500A) 187 hydrogen bonds defined for protein. 538 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: 0.51 Time building geometry restraints manager: 0.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 865 1.33 - 1.45: 607 1.45 - 1.57: 1904 1.57 - 1.69: 5 1.69 - 1.81: 27 Bond restraints: 3408 Sorted by residual: bond pdb=" O2B NDP A 501 " pdb=" P2B NDP A 501 " ideal model delta sigma weight residual 1.833 1.611 0.222 3.80e-02 6.93e+02 3.40e+01 bond pdb=" O5D NDP A 501 " pdb=" PN NDP A 501 " ideal model delta sigma weight residual 1.757 1.601 0.156 3.50e-02 8.16e+02 1.98e+01 bond pdb=" C1 AKG A 502 " pdb=" O2 AKG A 502 " ideal model delta sigma weight residual 1.239 1.308 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C2B NDP A 501 " pdb=" O2B NDP A 501 " ideal model delta sigma weight residual 1.330 1.424 -0.094 2.90e-02 1.19e+03 1.06e+01 bond pdb=" C LYS A 418 " pdb=" N LYS A 419 " ideal model delta sigma weight residual 1.329 1.369 -0.040 1.40e-02 5.10e+03 8.23e+00 ... (remaining 3403 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.59: 4611 5.59 - 11.18: 14 11.18 - 16.78: 2 16.78 - 22.37: 0 22.37 - 27.96: 1 Bond angle restraints: 4628 Sorted by residual: angle pdb=" PA NDP A 501 " pdb=" O3 NDP A 501 " pdb=" PN NDP A 501 " ideal model delta sigma weight residual 107.74 135.70 -27.96 1.95e+00 2.62e-01 2.05e+02 angle pdb=" C5B NDP A 501 " pdb=" O5B NDP A 501 " pdb=" PA NDP A 501 " ideal model delta sigma weight residual 103.84 119.42 -15.58 1.91e+00 2.73e-01 6.62e+01 angle pdb=" O1X NDP A 501 " pdb=" P2B NDP A 501 " pdb=" O3X NDP A 501 " ideal model delta sigma weight residual 117.46 111.72 5.74 1.17e+00 7.36e-01 2.42e+01 angle pdb=" O2N NDP A 501 " pdb=" PN NDP A 501 " pdb=" O5D NDP A 501 " ideal model delta sigma weight residual 100.52 109.00 -8.48 1.91e+00 2.74e-01 1.97e+01 angle pdb=" C5D NDP A 501 " pdb=" O5D NDP A 501 " pdb=" PN NDP A 501 " ideal model delta sigma weight residual 104.93 116.71 -11.78 2.66e+00 1.41e-01 1.96e+01 ... (remaining 4623 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 1696 17.52 - 35.03: 213 35.03 - 52.55: 73 52.55 - 70.06: 27 70.06 - 87.58: 10 Dihedral angle restraints: 2019 sinusoidal: 826 harmonic: 1193 Sorted by residual: dihedral pdb=" CA THR A 148 " pdb=" C THR A 148 " pdb=" N ASN A 149 " pdb=" CA ASN A 149 " ideal model delta harmonic sigma weight residual -180.00 -161.72 -18.28 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA ASP A 290 " pdb=" CB ASP A 290 " pdb=" CG ASP A 290 " pdb=" OD1 ASP A 290 " ideal model delta sinusoidal sigma weight residual -30.00 -88.81 58.81 1 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" CA ASP A 272 " pdb=" CB ASP A 272 " pdb=" CG ASP A 272 " pdb=" OD1 ASP A 272 " ideal model delta sinusoidal sigma weight residual -30.00 -88.28 58.28 1 2.00e+01 2.50e-03 1.14e+01 ... (remaining 2016 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 389 0.050 - 0.099: 87 0.099 - 0.149: 23 0.149 - 0.199: 1 0.199 - 0.248: 2 Chirality restraints: 502 Sorted by residual: chirality pdb=" C4D NDP A 501 " pdb=" C3D NDP A 501 " pdb=" C5D NDP A 501 " pdb=" O4D NDP A 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.47 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" C1B NDP A 501 " pdb=" C2B NDP A 501 " pdb=" N9A NDP A 501 " pdb=" O4B NDP A 501 " both_signs ideal model delta sigma weight residual False 2.59 2.37 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" C3B NDP A 501 " pdb=" C2B NDP A 501 " pdb=" C4B NDP A 501 " pdb=" O3B NDP A 501 " both_signs ideal model delta sigma weight residual False -2.75 -2.58 -0.17 2.00e-01 2.50e+01 6.92e-01 ... (remaining 499 not shown) Planarity restraints: 592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2N NDP A 501 " -0.067 2.00e-02 2.50e+03 4.30e-02 2.31e+01 pdb=" C3N NDP A 501 " -0.015 2.00e-02 2.50e+03 pdb=" C4N NDP A 501 " -0.010 2.00e-02 2.50e+03 pdb=" C7N NDP A 501 " 0.038 2.00e-02 2.50e+03 pdb=" N1N NDP A 501 " 0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C4N NDP A 501 " 0.013 2.00e-02 2.50e+03 2.17e-02 4.73e+00 pdb=" C5N NDP A 501 " -0.027 2.00e-02 2.50e+03 pdb=" C6N NDP A 501 " 0.028 2.00e-02 2.50e+03 pdb=" N1N NDP A 501 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 187 " 0.167 9.50e-02 1.11e+02 7.48e-02 3.44e+00 pdb=" NE ARG A 187 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG A 187 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 187 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 187 " 0.006 2.00e-02 2.50e+03 ... (remaining 589 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 1291 2.91 - 3.40: 3410 3.40 - 3.90: 6166 3.90 - 4.40: 6974 4.40 - 4.90: 11155 Nonbonded interactions: 28996 Sorted by model distance: nonbonded pdb=" OE1 GLU A 383 " pdb=" NH2 ARG A 406 " model vdw 2.408 3.120 nonbonded pdb=" OD1 ASP A 5 " pdb=" OG SER A 81 " model vdw 2.423 3.040 nonbonded pdb=" NE ARG A 73 " pdb=" OE1 GLU A 78 " model vdw 2.434 3.120 nonbonded pdb=" ND1 HIS A 388 " pdb=" O ILE A 393 " model vdw 2.446 3.120 nonbonded pdb=" NZ LYS A 69 " pdb=" OG1 THR A 175 " model vdw 2.506 3.120 ... (remaining 28991 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.660 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:6.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 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 0.222 3408 Z= 0.289 Angle : 0.967 27.959 4628 Z= 0.534 Chirality : 0.047 0.248 502 Planarity : 0.006 0.075 592 Dihedral : 19.343 87.579 1259 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.76 % Allowed : 25.00 % Favored : 73.24 % 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: 0.66 (0.42), residues: 417 helix: 1.80 (0.36), residues: 207 sheet: -0.68 (0.68), residues: 68 loop : -1.01 (0.50), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 118 TYR 0.015 0.001 TYR A 363 PHE 0.012 0.002 PHE A 381 TRP 0.009 0.001 TRP A 364 HIS 0.009 0.002 HIS A 394 Details of bonding type rmsd covalent geometry : bond 0.00722 ( 3408) covalent geometry : angle 0.96717 ( 4628) hydrogen bonds : bond 0.14815 ( 187) hydrogen bonds : angle 5.79629 ( 538) *********************** 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 73 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.092 Fit side-chains REVERT: A 213 LYS cc_start: 0.7494 (mmtp) cc_final: 0.7268 (mmmm) REVERT: A 272 ASP cc_start: 0.7401 (m-30) cc_final: 0.7057 (m-30) REVERT: A 312 LYS cc_start: 0.7503 (mttm) cc_final: 0.7293 (mptt) REVERT: A 333 LYS cc_start: 0.8075 (mtpt) cc_final: 0.7782 (mttp) REVERT: A 335 ILE cc_start: 0.8457 (mt) cc_final: 0.8127 (mm) outliers start: 6 outliers final: 2 residues processed: 71 average time/residue: 0.6498 time to fit residues: 47.2686 Evaluate side-chains 57 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 55 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 220 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 = 0.3594 r_free = 0.3594 target = 0.142541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.087975 restraints weight = 12728.149| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 2.71 r_work: 0.2724 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2616 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2616 r_free = 0.2616 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2616 r_free = 0.2616 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2616 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 3408 Z= 0.195 Angle : 0.584 6.706 4628 Z= 0.310 Chirality : 0.046 0.132 502 Planarity : 0.005 0.046 592 Dihedral : 6.663 52.087 471 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 5.88 % Allowed : 20.59 % Favored : 73.53 % 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: 0.71 (0.42), residues: 417 helix: 1.78 (0.35), residues: 210 sheet: -0.49 (0.74), residues: 60 loop : -1.00 (0.48), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 165 TYR 0.019 0.002 TYR A 363 PHE 0.015 0.002 PHE A 381 TRP 0.012 0.002 TRP A 364 HIS 0.004 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00464 ( 3408) covalent geometry : angle 0.58375 ( 4628) hydrogen bonds : bond 0.05625 ( 187) hydrogen bonds : angle 4.54796 ( 538) *********************** 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 82 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 62 time to evaluate : 0.185 Fit side-chains REVERT: A 272 ASP cc_start: 0.7367 (m-30) cc_final: 0.7014 (m-30) REVERT: A 286 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6844 (mp0) REVERT: A 312 LYS cc_start: 0.7642 (mttm) cc_final: 0.7375 (mptt) REVERT: A 333 LYS cc_start: 0.8238 (mtpt) cc_final: 0.7925 (mttp) REVERT: A 335 ILE cc_start: 0.8570 (mt) cc_final: 0.8249 (mm) REVERT: A 376 LYS cc_start: 0.9242 (OUTLIER) cc_final: 0.7252 (mptp) outliers start: 20 outliers final: 7 residues processed: 77 average time/residue: 0.7328 time to fit residues: 57.6858 Evaluate side-chains 67 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 220 TYR Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 376 LYS Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 389 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 39 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 26 optimal weight: 20.0000 chunk 30 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.145484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.096149 restraints weight = 6411.734| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.14 r_work: 0.2803 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2662 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2662 r_free = 0.2662 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2662 r_free = 0.2662 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2662 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3408 Z= 0.125 Angle : 0.514 8.516 4628 Z= 0.267 Chirality : 0.043 0.136 502 Planarity : 0.004 0.047 592 Dihedral : 6.299 55.614 470 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.24 % Allowed : 22.94 % Favored : 73.82 % 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: 0.90 (0.41), residues: 417 helix: 1.99 (0.35), residues: 211 sheet: -0.48 (0.72), residues: 62 loop : -1.00 (0.48), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 118 TYR 0.013 0.001 TYR A 363 PHE 0.012 0.002 PHE A 381 TRP 0.007 0.001 TRP A 263 HIS 0.003 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 3408) covalent geometry : angle 0.51371 ( 4628) hydrogen bonds : bond 0.04508 ( 187) hydrogen bonds : angle 4.23507 ( 538) *********************** 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 70 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.093 Fit side-chains REVERT: A 272 ASP cc_start: 0.7413 (m-30) cc_final: 0.7123 (m-30) REVERT: A 286 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6828 (mp0) REVERT: A 312 LYS cc_start: 0.7704 (mttm) cc_final: 0.7442 (mptt) REVERT: A 333 LYS cc_start: 0.8241 (mtpt) cc_final: 0.7896 (mtpp) REVERT: A 335 ILE cc_start: 0.8532 (mt) cc_final: 0.8205 (mm) REVERT: A 376 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.7305 (mptp) outliers start: 11 outliers final: 3 residues processed: 67 average time/residue: 0.7073 time to fit residues: 48.4244 Evaluate side-chains 61 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 376 LYS 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 24 optimal weight: 5.9990 chunk 7 optimal weight: 0.0770 chunk 39 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 37 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 overall best weight: 2.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.143742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.094884 restraints weight = 12242.105| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 3.65 r_work: 0.2707 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2675 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2675 r_free = 0.2675 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2675 r_free = 0.2675 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2675 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3408 Z= 0.152 Angle : 0.539 8.234 4628 Z= 0.281 Chirality : 0.044 0.131 502 Planarity : 0.005 0.048 592 Dihedral : 5.638 51.356 468 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.65 % Allowed : 23.53 % Favored : 73.82 % 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: 0.91 (0.41), residues: 417 helix: 2.08 (0.35), residues: 205 sheet: -0.40 (0.72), residues: 62 loop : -1.05 (0.46), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 165 TYR 0.015 0.001 TYR A 363 PHE 0.013 0.002 PHE A 381 TRP 0.008 0.001 TRP A 382 HIS 0.004 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 3408) covalent geometry : angle 0.53947 ( 4628) hydrogen bonds : bond 0.04994 ( 187) hydrogen bonds : angle 4.24168 ( 538) *********************** 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 65 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.084 Fit side-chains REVERT: A 272 ASP cc_start: 0.7338 (m-30) cc_final: 0.7047 (m-30) REVERT: A 286 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6799 (mp0) REVERT: A 312 LYS cc_start: 0.7637 (mttm) cc_final: 0.7343 (mptt) REVERT: A 333 LYS cc_start: 0.8203 (mtpt) cc_final: 0.7851 (mtpp) REVERT: A 335 ILE cc_start: 0.8501 (mt) cc_final: 0.8177 (mm) REVERT: A 376 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.7182 (mptp) outliers start: 9 outliers final: 5 residues processed: 64 average time/residue: 0.7021 time to fit residues: 45.9299 Evaluate side-chains 63 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 220 TYR Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 376 LYS Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 389 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 33 optimal weight: 0.8980 chunk 25 optimal weight: 20.0000 chunk 24 optimal weight: 7.9990 chunk 6 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 193 GLN A 337 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.147618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.098384 restraints weight = 12901.562| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 3.75 r_work: 0.2782 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2754 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2754 r_free = 0.2754 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2754 r_free = 0.2754 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2754 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3408 Z= 0.104 Angle : 0.493 7.555 4628 Z= 0.253 Chirality : 0.042 0.129 502 Planarity : 0.004 0.049 592 Dihedral : 5.378 56.993 468 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 3.24 % Allowed : 22.94 % Favored : 73.82 % 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: 1.14 (0.42), residues: 417 helix: 2.15 (0.35), residues: 211 sheet: -0.22 (0.73), residues: 62 loop : -0.92 (0.48), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 165 TYR 0.009 0.001 TYR A 363 PHE 0.009 0.001 PHE A 381 TRP 0.008 0.001 TRP A 263 HIS 0.002 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 3408) covalent geometry : angle 0.49327 ( 4628) hydrogen bonds : bond 0.03913 ( 187) hydrogen bonds : angle 4.02370 ( 538) *********************** 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 67 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.080 Fit side-chains REVERT: A 193 GLN cc_start: 0.8888 (tp-100) cc_final: 0.8529 (tp40) REVERT: A 218 GLN cc_start: 0.8120 (tm-30) cc_final: 0.7358 (tm-30) REVERT: A 272 ASP cc_start: 0.7392 (m-30) cc_final: 0.7113 (m-30) REVERT: A 312 LYS cc_start: 0.7656 (mttm) cc_final: 0.7381 (mptt) REVERT: A 335 ILE cc_start: 0.8374 (mt) cc_final: 0.8046 (mm) REVERT: A 376 LYS cc_start: 0.9076 (OUTLIER) cc_final: 0.7292 (mptp) outliers start: 11 outliers final: 5 residues processed: 67 average time/residue: 0.7140 time to fit residues: 48.9014 Evaluate side-chains 62 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 220 TYR Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 376 LYS Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 12 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 10.0000 chunk 13 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 7 optimal weight: 0.1980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.148749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.099158 restraints weight = 6400.113| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.20 r_work: 0.2855 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2737 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2737 r_free = 0.2737 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2737 r_free = 0.2737 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2737 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3408 Z= 0.100 Angle : 0.486 6.710 4628 Z= 0.248 Chirality : 0.042 0.125 502 Planarity : 0.004 0.048 592 Dihedral : 5.195 56.682 468 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.76 % Allowed : 25.00 % Favored : 73.24 % 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: 1.24 (0.42), residues: 417 helix: 2.22 (0.35), residues: 211 sheet: -0.17 (0.73), residues: 62 loop : -0.84 (0.49), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 406 TYR 0.008 0.001 TYR A 363 PHE 0.008 0.001 PHE A 381 TRP 0.007 0.001 TRP A 63 HIS 0.002 0.000 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 3408) covalent geometry : angle 0.48601 ( 4628) hydrogen bonds : bond 0.03750 ( 187) hydrogen bonds : angle 3.92014 ( 538) *********************** 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 63 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.133 Fit side-chains REVERT: A 32 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8797 (mtpt) REVERT: A 193 GLN cc_start: 0.8940 (tp-100) cc_final: 0.8665 (tp40) REVERT: A 218 GLN cc_start: 0.8206 (tm-30) cc_final: 0.7508 (tm-30) REVERT: A 272 ASP cc_start: 0.7326 (m-30) cc_final: 0.7082 (m-30) REVERT: A 312 LYS cc_start: 0.7772 (mttm) cc_final: 0.7518 (mptt) REVERT: A 335 ILE cc_start: 0.8346 (mt) cc_final: 0.7985 (mm) REVERT: A 376 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.7413 (mptp) outliers start: 6 outliers final: 2 residues processed: 63 average time/residue: 0.7088 time to fit residues: 45.6154 Evaluate side-chains 60 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 376 LYS Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 37 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 10 optimal weight: 0.2980 chunk 21 optimal weight: 0.3980 chunk 38 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.149904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.100461 restraints weight = 13980.385| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 3.86 r_work: 0.2822 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2814 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2814 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3408 Z= 0.097 Angle : 0.482 7.175 4628 Z= 0.244 Chirality : 0.041 0.124 502 Planarity : 0.004 0.048 592 Dihedral : 5.058 57.487 468 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.88 % Allowed : 25.59 % Favored : 73.53 % 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: 1.34 (0.42), residues: 417 helix: 2.23 (0.35), residues: 214 sheet: -0.14 (0.73), residues: 62 loop : -0.74 (0.50), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 331 TYR 0.007 0.001 TYR A 363 PHE 0.007 0.001 PHE A 341 TRP 0.006 0.001 TRP A 63 HIS 0.002 0.000 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00214 ( 3408) covalent geometry : angle 0.48164 ( 4628) hydrogen bonds : bond 0.03572 ( 187) hydrogen bonds : angle 3.84853 ( 538) *********************** 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 62 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.137 Fit side-chains REVERT: A 32 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8742 (mtpt) REVERT: A 218 GLN cc_start: 0.8175 (tm-30) cc_final: 0.7450 (tm-30) REVERT: A 272 ASP cc_start: 0.7374 (m-30) cc_final: 0.7080 (m-30) REVERT: A 300 VAL cc_start: 0.8306 (m) cc_final: 0.8093 (p) REVERT: A 312 LYS cc_start: 0.7690 (mttm) cc_final: 0.7420 (mptt) REVERT: A 335 ILE cc_start: 0.8289 (mt) cc_final: 0.7932 (mm) outliers start: 3 outliers final: 1 residues processed: 62 average time/residue: 0.6877 time to fit residues: 43.5765 Evaluate side-chains 58 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 148 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 20.0000 chunk 22 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 30 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.146950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.094390 restraints weight = 5205.717| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 1.80 r_work: 0.2834 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2709 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2709 r_free = 0.2709 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2709 r_free = 0.2709 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2709 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3408 Z= 0.125 Angle : 0.522 7.539 4628 Z= 0.266 Chirality : 0.043 0.121 502 Planarity : 0.005 0.049 592 Dihedral : 5.234 54.016 468 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.47 % Allowed : 25.59 % Favored : 72.94 % 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: 1.26 (0.42), residues: 417 helix: 2.21 (0.35), residues: 212 sheet: -0.29 (0.72), residues: 62 loop : -0.73 (0.51), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 331 TYR 0.011 0.001 TYR A 363 PHE 0.010 0.001 PHE A 381 TRP 0.006 0.001 TRP A 63 HIS 0.002 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 3408) covalent geometry : angle 0.52189 ( 4628) hydrogen bonds : bond 0.04252 ( 187) hydrogen bonds : angle 3.97724 ( 538) *********************** 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 59 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.100 Fit side-chains REVERT: A 32 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8795 (mtpt) REVERT: A 218 GLN cc_start: 0.8227 (tm-30) cc_final: 0.7499 (tm-30) REVERT: A 272 ASP cc_start: 0.7383 (m-30) cc_final: 0.7131 (m-30) REVERT: A 312 LYS cc_start: 0.7793 (mttm) cc_final: 0.7555 (mptt) REVERT: A 335 ILE cc_start: 0.8370 (mt) cc_final: 0.8024 (mm) REVERT: A 376 LYS cc_start: 0.9152 (OUTLIER) cc_final: 0.7341 (mptp) outliers start: 5 outliers final: 1 residues processed: 59 average time/residue: 0.6986 time to fit residues: 42.1665 Evaluate side-chains 55 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 376 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 27 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 31 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 388 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.148730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.098539 restraints weight = 6805.410| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.28 r_work: 0.2823 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2723 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2723 r_free = 0.2723 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2723 r_free = 0.2723 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2723 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 3408 Z= 0.106 Angle : 0.502 7.128 4628 Z= 0.254 Chirality : 0.042 0.127 502 Planarity : 0.004 0.049 592 Dihedral : 5.133 55.959 468 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.47 % Allowed : 25.88 % Favored : 72.65 % 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: 1.31 (0.42), residues: 417 helix: 2.19 (0.35), residues: 214 sheet: -0.19 (0.72), residues: 62 loop : -0.67 (0.52), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 331 TYR 0.009 0.001 TYR A 363 PHE 0.008 0.001 PHE A 381 TRP 0.006 0.001 TRP A 63 HIS 0.004 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 3408) covalent geometry : angle 0.50156 ( 4628) hydrogen bonds : bond 0.03803 ( 187) hydrogen bonds : angle 3.91639 ( 538) *********************** 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: 5 poor density : 55 time to evaluate : 0.131 Fit side-chains REVERT: A 32 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8799 (mtpt) REVERT: A 146 VAL cc_start: 0.8433 (p) cc_final: 0.8227 (m) REVERT: A 218 GLN cc_start: 0.8207 (tm-30) cc_final: 0.7490 (tm-30) REVERT: A 272 ASP cc_start: 0.7359 (m-30) cc_final: 0.7104 (m-30) REVERT: A 300 VAL cc_start: 0.8365 (m) cc_final: 0.8114 (p) REVERT: A 312 LYS cc_start: 0.7778 (mttm) cc_final: 0.7535 (mptt) REVERT: A 335 ILE cc_start: 0.8339 (mt) cc_final: 0.7986 (mm) REVERT: A 376 LYS cc_start: 0.9134 (OUTLIER) cc_final: 0.7401 (mptp) outliers start: 5 outliers final: 3 residues processed: 60 average time/residue: 0.6580 time to fit residues: 40.4985 Evaluate side-chains 60 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 220 TYR Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 376 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 15 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 32 optimal weight: 20.0000 chunk 35 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.145252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.095195 restraints weight = 11408.548| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 3.28 r_work: 0.2742 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2618 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2618 r_free = 0.2618 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2618 r_free = 0.2618 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2618 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3408 Z= 0.151 Angle : 0.549 7.047 4628 Z= 0.282 Chirality : 0.044 0.131 502 Planarity : 0.005 0.049 592 Dihedral : 5.365 51.852 468 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.76 % Allowed : 25.59 % Favored : 72.65 % 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: 1.22 (0.42), residues: 417 helix: 2.28 (0.35), residues: 206 sheet: -0.25 (0.72), residues: 62 loop : -0.83 (0.49), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 118 TYR 0.013 0.001 TYR A 363 PHE 0.013 0.002 PHE A 381 TRP 0.006 0.001 TRP A 364 HIS 0.005 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 3408) covalent geometry : angle 0.54949 ( 4628) hydrogen bonds : bond 0.04649 ( 187) hydrogen bonds : angle 4.06457 ( 538) ********************** 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 60 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.094 Fit side-chains REVERT: A 32 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8831 (mtpt) REVERT: A 218 GLN cc_start: 0.8230 (tm-30) cc_final: 0.7583 (tm-30) REVERT: A 272 ASP cc_start: 0.7386 (m-30) cc_final: 0.7123 (m-30) REVERT: A 312 LYS cc_start: 0.7798 (mttm) cc_final: 0.7544 (mptt) REVERT: A 335 ILE cc_start: 0.8374 (mt) cc_final: 0.8008 (mm) REVERT: A 376 LYS cc_start: 0.9176 (OUTLIER) cc_final: 0.7325 (mptp) outliers start: 6 outliers final: 3 residues processed: 60 average time/residue: 0.6853 time to fit residues: 42.1626 Evaluate side-chains 58 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 220 TYR Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 376 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 8 optimal weight: 1.9990 chunk 4 optimal weight: 0.0020 chunk 25 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 30 optimal weight: 8.9990 overall best weight: 1.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.146372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.096125 restraints weight = 7701.107| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 2.50 r_work: 0.2783 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2666 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2666 r_free = 0.2666 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2666 r_free = 0.2666 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2666 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3408 Z= 0.127 Angle : 0.539 9.092 4628 Z= 0.273 Chirality : 0.043 0.129 502 Planarity : 0.005 0.049 592 Dihedral : 5.324 53.160 468 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.47 % Allowed : 25.88 % Favored : 72.65 % 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: 1.21 (0.42), residues: 417 helix: 2.17 (0.35), residues: 212 sheet: -0.25 (0.72), residues: 62 loop : -0.79 (0.50), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 331 TYR 0.012 0.001 TYR A 363 PHE 0.011 0.001 PHE A 381 TRP 0.006 0.001 TRP A 63 HIS 0.004 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 3408) covalent geometry : angle 0.53897 ( 4628) hydrogen bonds : bond 0.04286 ( 187) hydrogen bonds : angle 4.05616 ( 538) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1770.36 seconds wall clock time: 30 minutes 52.39 seconds (1852.39 seconds total)