Starting phenix.real_space_refine on Wed Sep 17 03:41:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8znb_60266/09_2025/8znb_60266.cif Found real_map, /net/cci-nas-00/data/ceres_data/8znb_60266/09_2025/8znb_60266.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8znb_60266/09_2025/8znb_60266.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8znb_60266/09_2025/8znb_60266.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8znb_60266/09_2025/8znb_60266.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8znb_60266/09_2025/8znb_60266.map" } resolution = 2.53 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 2113 2.51 5 N 564 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 15 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: 3342 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: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 69 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1, 'water': 21} Link IDs: {None: 21} 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: 1.39, per 1000 atoms: 0.42 Number of scatterers: 3342 At special positions: 0 Unit cell: (66.176, 61.664, 73.696, 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 564 7.00 C 2113 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: 0.19 Conformation dependent library (CDL) restraints added in 200.0 milliseconds Enol-peptide restraints added in 476.8 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 3 sheets defined 56.0% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 5 through 19 removed outlier: 3.745A pdb=" N GLN A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 33 removed outlier: 3.795A pdb=" N LYS A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 97 removed outlier: 3.722A pdb=" N TRP A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 4.084A 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: 3.565A 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 235 removed outlier: 3.701A pdb=" N TYR A 226 " --> pdb=" O ASN A 222 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LEU A 235 " --> pdb=" O ALA A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 280 through 286 removed outlier: 4.008A pdb=" N GLU A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 306 removed outlier: 3.676A pdb=" N ALA A 306 " --> pdb=" O GLU A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 333 removed outlier: 3.548A pdb=" N GLU A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS A 333 " --> pdb=" O ILE A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 344 removed outlier: 3.985A pdb=" N ASN A 344 " --> pdb=" O ASP A 340 " (cutoff:3.500A) 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: 6.664A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 6.439A 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: 6.664A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N LYS A 69 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N GLY A 106 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N THR A 68 " --> pdb=" O ILE A 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 248 through 250 removed outlier: 7.291A pdb=" N ILE A 215 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N VAL A 242 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N VAL A 217 " --> pdb=" O VAL A 242 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LYS A 214 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ALA A 293 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ALA A 216 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU A 292 " --> pdb=" O ALA A 315 " (cutoff:3.500A) 188 hydrogen bonds defined for protein. 547 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: 0.54 Time building geometry restraints manager: 0.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 938 1.33 - 1.45: 548 1.45 - 1.57: 1881 1.57 - 1.69: 5 1.69 - 1.81: 27 Bond restraints: 3399 Sorted by residual: bond pdb=" O2B NDP A 500 " pdb=" P2B NDP A 500 " ideal model delta sigma weight residual 1.833 1.612 0.221 3.80e-02 6.93e+02 3.38e+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 1.93e+01 bond pdb=" C PRO A 252 " pdb=" N ASP A 253 " ideal model delta sigma weight residual 1.335 1.384 -0.050 1.36e-02 5.41e+03 1.33e+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 1.02e+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 6.22e+00 ... (remaining 3394 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.88: 4599 4.88 - 9.76: 14 9.76 - 14.64: 2 14.64 - 19.52: 1 19.52 - 24.40: 1 Bond angle restraints: 4617 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 107.74 132.14 -24.40 1.95e+00 2.62e-01 1.56e+02 angle pdb=" C5B NDP A 500 " pdb=" O5B NDP A 500 " pdb=" PA NDP A 500 " ideal model delta sigma weight residual 103.84 118.94 -15.10 1.91e+00 2.73e-01 6.22e+01 angle pdb=" C5D NDP A 500 " pdb=" O5D NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 104.93 119.33 -14.40 2.66e+00 1.41e-01 2.93e+01 angle pdb=" O2N NDP A 500 " pdb=" PN NDP A 500 " pdb=" O5D NDP A 500 " ideal model delta sigma weight residual 100.52 109.57 -9.05 1.91e+00 2.74e-01 2.24e+01 angle pdb=" O1X NDP A 500 " pdb=" P2B NDP A 500 " pdb=" O3X NDP A 500 " ideal model delta sigma weight residual 117.46 112.31 5.15 1.17e+00 7.36e-01 1.95e+01 ... (remaining 4612 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 1819 17.98 - 35.97: 143 35.97 - 53.95: 36 53.95 - 71.94: 10 71.94 - 89.92: 7 Dihedral angle restraints: 2015 sinusoidal: 822 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 -162.76 -17.24 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA TYR A 101 " pdb=" C TYR A 101 " pdb=" N GLY A 102 " pdb=" CA GLY A 102 " ideal model delta harmonic sigma weight residual 180.00 163.45 16.55 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CB GLU A 303 " pdb=" CG GLU A 303 " pdb=" CD GLU A 303 " pdb=" OE1 GLU A 303 " ideal model delta sinusoidal sigma weight residual 0.00 88.04 -88.04 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 2012 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 400 0.052 - 0.104: 84 0.104 - 0.156: 16 0.156 - 0.208: 1 0.208 - 0.260: 1 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 -2.45 -0.26 2.00e-01 2.50e+01 1.69e+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 2.41 0.18 2.00e-01 2.50e+01 8.02e-01 chirality pdb=" C2D NDP A 500 " pdb=" C1D NDP A 500 " pdb=" C3D NDP A 500 " pdb=" O2D NDP A 500 " both_signs ideal model delta sigma weight residual False -2.71 -2.56 -0.15 2.00e-01 2.50e+01 5.29e-01 ... (remaining 499 not shown) Planarity restraints: 589 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 149 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.13e+00 pdb=" N PRO A 150 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 150 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 150 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 393 " 0.007 2.00e-02 2.50e+03 1.38e-02 1.90e+00 pdb=" C ILE A 393 " -0.024 2.00e-02 2.50e+03 pdb=" O ILE A 393 " 0.009 2.00e-02 2.50e+03 pdb=" N HIS A 394 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 394 " -0.013 2.00e-02 2.50e+03 1.09e-02 1.79e+00 pdb=" CG HIS A 394 " 0.021 2.00e-02 2.50e+03 pdb=" ND1 HIS A 394 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 HIS A 394 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 HIS A 394 " 0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS A 394 " -0.011 2.00e-02 2.50e+03 ... (remaining 586 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 1290 2.92 - 3.41: 3444 3.41 - 3.91: 5994 3.91 - 4.40: 6792 4.40 - 4.90: 10962 Nonbonded interactions: 28482 Sorted by model distance: nonbonded pdb=" NE ARG A 65 " pdb=" O HOH A 601 " model vdw 2.421 3.120 nonbonded pdb=" OH TYR A 408 " pdb=" O LYS A 419 " model vdw 2.443 3.040 nonbonded pdb=" OE1 GLU A 354 " pdb=" O HOH A 602 " model vdw 2.449 3.040 nonbonded pdb=" NZ LYS A 177 " pdb=" OD1 ASN A 358 " model vdw 2.449 3.120 nonbonded pdb=" NZ LYS A 177 " pdb=" OE2 GLU A 354 " model vdw 2.464 3.120 ... (remaining 28477 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: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.050 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 5.250 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:8.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 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 0.221 3399 Z= 0.286 Angle : 0.945 24.400 4617 Z= 0.541 Chirality : 0.047 0.260 502 Planarity : 0.005 0.045 589 Dihedral : 15.547 89.920 1255 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.06 % Allowed : 0.59 % Favored : 97.35 % 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: 0.61 (0.41), residues: 417 helix: 1.83 (0.37), residues: 202 sheet: -0.52 (0.69), residues: 64 loop : -1.15 (0.45), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 118 TYR 0.013 0.002 TYR A 226 PHE 0.010 0.002 PHE A 341 TRP 0.016 0.001 TRP A 92 HIS 0.008 0.002 HIS A 394 Details of bonding type rmsd covalent geometry : bond 0.00699 ( 3399) covalent geometry : angle 0.94544 ( 4617) hydrogen bonds : bond 0.12910 ( 173) hydrogen bonds : angle 6.18451 ( 547) *********************** 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 87 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.076 Fit side-chains REVERT: A 187 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.7563 (ttm110) REVERT: A 333 LYS cc_start: 0.8444 (mtpp) cc_final: 0.8192 (mtpt) REVERT: A 386 ASN cc_start: 0.8503 (m-40) cc_final: 0.8166 (m110) REVERT: A 388 HIS cc_start: 0.8934 (OUTLIER) cc_final: 0.7957 (t70) outliers start: 7 outliers final: 0 residues processed: 86 average time/residue: 0.6045 time to fit residues: 53.2873 Evaluate side-chains 59 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 HIS ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.132792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.086484 restraints weight = 13553.334| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 3.01 r_work: 0.2693 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2580 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2572 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2572 r_free = 0.2572 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2572 r_free = 0.2572 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2572 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8953 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 3399 Z= 0.229 Angle : 0.608 9.034 4617 Z= 0.323 Chirality : 0.049 0.160 502 Planarity : 0.005 0.047 589 Dihedral : 6.757 56.549 470 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.24 % Allowed : 10.88 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.41), residues: 417 helix: 1.71 (0.36), residues: 209 sheet: -0.41 (0.68), residues: 67 loop : -0.94 (0.47), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 129 TYR 0.020 0.002 TYR A 363 PHE 0.012 0.002 PHE A 341 TRP 0.010 0.002 TRP A 382 HIS 0.003 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00567 ( 3399) covalent geometry : angle 0.60801 ( 4617) hydrogen bonds : bond 0.05475 ( 173) hydrogen bonds : angle 4.45632 ( 547) *********************** 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 77 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.133 Fit side-chains REVERT: A 187 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.7732 (ttm110) REVERT: A 214 LYS cc_start: 0.8570 (mttm) cc_final: 0.8218 (mttp) REVERT: A 297 ILE cc_start: 0.8677 (OUTLIER) cc_final: 0.8327 (pp) REVERT: A 333 LYS cc_start: 0.8651 (mtpp) cc_final: 0.8433 (mtpt) REVERT: A 370 ARG cc_start: 0.8373 (ttp-110) cc_final: 0.8167 (ttm110) REVERT: A 383 GLU cc_start: 0.8488 (tt0) cc_final: 0.8074 (mt-10) REVERT: A 388 HIS cc_start: 0.9047 (OUTLIER) cc_final: 0.7819 (t70) outliers start: 11 outliers final: 3 residues processed: 71 average time/residue: 0.6843 time to fit residues: 49.7609 Evaluate side-chains 65 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 297 ILE 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 31 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 20 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 7 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 17 optimal weight: 0.0570 chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.136757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.095219 restraints weight = 5991.687| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 1.92 r_work: 0.2825 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2709 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2709 r_free = 0.2709 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2709 r_free = 0.2709 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2709 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3399 Z= 0.111 Angle : 0.515 6.621 4617 Z= 0.267 Chirality : 0.044 0.143 502 Planarity : 0.004 0.047 589 Dihedral : 6.246 53.979 470 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.65 % Allowed : 14.41 % Favored : 82.94 % 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: 0.92 (0.42), residues: 417 helix: 2.01 (0.36), residues: 206 sheet: -0.34 (0.71), residues: 64 loop : -0.96 (0.46), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 187 TYR 0.010 0.001 TYR A 363 PHE 0.007 0.001 PHE A 341 TRP 0.007 0.001 TRP A 92 HIS 0.002 0.000 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 3399) covalent geometry : angle 0.51488 ( 4617) hydrogen bonds : bond 0.03820 ( 173) hydrogen bonds : angle 3.97009 ( 547) *********************** 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 67 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.129 Fit side-chains REVERT: A 8 GLU cc_start: 0.7792 (pt0) cc_final: 0.7313 (tt0) REVERT: A 214 LYS cc_start: 0.8796 (mttm) cc_final: 0.8413 (mttt) REVERT: A 218 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8421 (tp40) REVERT: A 252 PRO cc_start: 0.8069 (Cg_endo) cc_final: 0.7851 (Cg_exo) REVERT: A 297 ILE cc_start: 0.8676 (pp) cc_final: 0.8421 (pp) REVERT: A 333 LYS cc_start: 0.8630 (mtpp) cc_final: 0.8412 (mtpt) REVERT: A 383 GLU cc_start: 0.8150 (tt0) cc_final: 0.7760 (mt-10) REVERT: A 388 HIS cc_start: 0.8884 (OUTLIER) cc_final: 0.7878 (t70) outliers start: 9 outliers final: 1 residues processed: 63 average time/residue: 0.6377 time to fit residues: 41.2154 Evaluate side-chains 58 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 270 VAL 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: 0.9990 chunk 31 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 28 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.134235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.092069 restraints weight = 7189.026| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 2.10 r_work: 0.2755 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2630 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2630 r_free = 0.2630 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2630 r_free = 0.2630 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2630 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3399 Z= 0.140 Angle : 0.549 7.417 4617 Z= 0.285 Chirality : 0.045 0.152 502 Planarity : 0.005 0.047 589 Dihedral : 5.633 57.174 466 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.65 % Allowed : 14.71 % Favored : 82.65 % 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: 0.88 (0.42), residues: 417 helix: 2.03 (0.36), residues: 205 sheet: -0.59 (0.68), residues: 69 loop : -0.91 (0.47), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 129 TYR 0.012 0.001 TYR A 363 PHE 0.010 0.002 PHE A 341 TRP 0.007 0.001 TRP A 382 HIS 0.002 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 3399) covalent geometry : angle 0.54889 ( 4617) hydrogen bonds : bond 0.04332 ( 173) hydrogen bonds : angle 3.98546 ( 547) *********************** 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 67 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.084 Fit side-chains REVERT: A 214 LYS cc_start: 0.8826 (mttm) cc_final: 0.8461 (mttp) REVERT: A 218 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8376 (tp40) REVERT: A 252 PRO cc_start: 0.8059 (Cg_endo) cc_final: 0.7798 (Cg_exo) REVERT: A 297 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8354 (pp) REVERT: A 383 GLU cc_start: 0.8257 (tt0) cc_final: 0.7798 (mt-10) REVERT: A 388 HIS cc_start: 0.8916 (OUTLIER) cc_final: 0.7895 (t70) REVERT: A 419 LYS cc_start: 0.8342 (mttp) cc_final: 0.8077 (mttp) outliers start: 9 outliers final: 2 residues processed: 60 average time/residue: 0.5886 time to fit residues: 36.1883 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 : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.134922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.092682 restraints weight = 15674.395| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 3.52 r_work: 0.2743 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2694 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2694 r_free = 0.2694 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2694 r_free = 0.2694 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2694 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3399 Z= 0.119 Angle : 0.514 6.143 4617 Z= 0.266 Chirality : 0.044 0.150 502 Planarity : 0.005 0.047 589 Dihedral : 5.607 59.962 466 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.65 % Allowed : 15.29 % Favored : 82.06 % 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: 0.88 (0.42), residues: 417 helix: 2.04 (0.36), residues: 206 sheet: -0.54 (0.68), residues: 69 loop : -1.00 (0.46), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 122 TYR 0.011 0.001 TYR A 363 PHE 0.009 0.001 PHE A 341 TRP 0.006 0.001 TRP A 30 HIS 0.002 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 3399) covalent geometry : angle 0.51356 ( 4617) hydrogen bonds : bond 0.03922 ( 173) hydrogen bonds : angle 3.86319 ( 547) *********************** 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 66 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.095 Fit side-chains REVERT: A 214 LYS cc_start: 0.8861 (mttm) cc_final: 0.8523 (mttp) REVERT: A 252 PRO cc_start: 0.8097 (Cg_endo) cc_final: 0.7894 (Cg_exo) REVERT: A 297 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8315 (pp) REVERT: A 383 GLU cc_start: 0.8113 (tt0) cc_final: 0.7660 (mt-10) REVERT: A 388 HIS cc_start: 0.8868 (OUTLIER) cc_final: 0.7770 (t70) REVERT: A 419 LYS cc_start: 0.8323 (mttp) cc_final: 0.8101 (mttp) outliers start: 9 outliers final: 1 residues processed: 60 average time/residue: 0.5535 time to fit residues: 34.1261 Evaluate side-chains 60 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 297 ILE 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 38 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 32 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.131208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.088086 restraints weight = 8268.863| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 2.29 r_work: 0.2732 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2597 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2597 r_free = 0.2597 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2597 r_free = 0.2597 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2597 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8954 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3399 Z= 0.161 Angle : 0.581 10.949 4617 Z= 0.293 Chirality : 0.046 0.161 502 Planarity : 0.005 0.046 589 Dihedral : 5.842 58.859 466 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.88 % Allowed : 17.65 % Favored : 81.47 % 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: 0.91 (0.42), residues: 417 helix: 1.95 (0.36), residues: 208 sheet: -0.24 (0.71), residues: 63 loop : -0.97 (0.46), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 73 TYR 0.015 0.002 TYR A 363 PHE 0.012 0.002 PHE A 341 TRP 0.008 0.001 TRP A 382 HIS 0.002 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 3399) covalent geometry : angle 0.58052 ( 4617) hydrogen bonds : bond 0.04692 ( 173) hydrogen bonds : angle 4.03002 ( 547) *********************** 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 61 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.118 Fit side-chains REVERT: A 214 LYS cc_start: 0.8933 (mttm) cc_final: 0.8583 (mttp) REVERT: A 252 PRO cc_start: 0.8192 (Cg_endo) cc_final: 0.7979 (Cg_exo) REVERT: A 297 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8421 (pp) REVERT: A 367 GLU cc_start: 0.8440 (mp0) cc_final: 0.8186 (mp0) REVERT: A 383 GLU cc_start: 0.8328 (tt0) cc_final: 0.7894 (mt-10) REVERT: A 388 HIS cc_start: 0.9023 (OUTLIER) cc_final: 0.7803 (t70) outliers start: 3 outliers final: 1 residues processed: 59 average time/residue: 0.6111 time to fit residues: 36.9958 Evaluate side-chains 59 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 297 ILE 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 30 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 32 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 4 optimal weight: 0.0000 chunk 29 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 18 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.135187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.091467 restraints weight = 8097.509| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.40 r_work: 0.2793 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2680 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2680 r_free = 0.2680 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2680 r_free = 0.2680 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2680 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3399 Z= 0.112 Angle : 0.528 9.204 4617 Z= 0.269 Chirality : 0.044 0.150 502 Planarity : 0.004 0.046 589 Dihedral : 5.518 57.332 466 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.18 % Allowed : 17.06 % Favored : 81.76 % 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 (0.42), residues: 417 helix: 2.02 (0.37), residues: 208 sheet: -0.18 (0.72), residues: 63 loop : -0.91 (0.47), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 73 TYR 0.009 0.001 TYR A 363 PHE 0.010 0.001 PHE A 341 TRP 0.007 0.001 TRP A 74 HIS 0.002 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 3399) covalent geometry : angle 0.52825 ( 4617) hydrogen bonds : bond 0.03717 ( 173) hydrogen bonds : angle 3.79499 ( 547) *********************** 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: 4 poor density : 58 time to evaluate : 0.131 Fit side-chains REVERT: A 214 LYS cc_start: 0.8949 (mttm) cc_final: 0.8582 (mttp) REVERT: A 297 ILE cc_start: 0.8620 (OUTLIER) cc_final: 0.8374 (pp) REVERT: A 367 GLU cc_start: 0.8338 (mp0) cc_final: 0.8050 (mp0) REVERT: A 383 GLU cc_start: 0.8264 (tt0) cc_final: 0.7784 (mt-10) REVERT: A 388 HIS cc_start: 0.8877 (OUTLIER) cc_final: 0.7729 (t70) outliers start: 4 outliers final: 1 residues processed: 60 average time/residue: 0.6072 time to fit residues: 37.4521 Evaluate side-chains 57 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 26 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.133185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.088272 restraints weight = 12201.498| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 2.92 r_work: 0.2725 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2598 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2598 r_free = 0.2598 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2598 r_free = 0.2598 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2598 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3399 Z= 0.129 Angle : 0.551 9.494 4617 Z= 0.279 Chirality : 0.044 0.161 502 Planarity : 0.005 0.045 589 Dihedral : 5.632 57.240 466 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.88 % Allowed : 17.94 % Favored : 81.18 % 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: 1.00 (0.42), residues: 417 helix: 2.03 (0.36), residues: 208 sheet: -0.15 (0.72), residues: 63 loop : -0.97 (0.46), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 129 TYR 0.011 0.001 TYR A 363 PHE 0.009 0.002 PHE A 341 TRP 0.007 0.001 TRP A 30 HIS 0.002 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 3399) covalent geometry : angle 0.55056 ( 4617) hydrogen bonds : bond 0.04128 ( 173) hydrogen bonds : angle 3.86068 ( 547) *********************** 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: 3 poor density : 55 time to evaluate : 0.083 Fit side-chains REVERT: A 211 LYS cc_start: 0.7955 (mtmm) cc_final: 0.7726 (mttt) REVERT: A 214 LYS cc_start: 0.8964 (mttm) cc_final: 0.8545 (mttt) REVERT: A 297 ILE cc_start: 0.8637 (OUTLIER) cc_final: 0.8353 (pp) REVERT: A 367 GLU cc_start: 0.8429 (mp0) cc_final: 0.8125 (mp0) REVERT: A 383 GLU cc_start: 0.8386 (tt0) cc_final: 0.7888 (mt-10) REVERT: A 388 HIS cc_start: 0.8930 (OUTLIER) cc_final: 0.7861 (t70) outliers start: 3 outliers final: 1 residues processed: 56 average time/residue: 0.5446 time to fit residues: 31.3768 Evaluate side-chains 59 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 17 optimal weight: 0.1980 chunk 38 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.135178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.090288 restraints weight = 12921.435| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 3.02 r_work: 0.2751 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2652 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2652 r_free = 0.2652 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2652 r_free = 0.2652 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2652 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3399 Z= 0.113 Angle : 0.537 9.052 4617 Z= 0.271 Chirality : 0.043 0.158 502 Planarity : 0.004 0.045 589 Dihedral : 5.492 56.561 466 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.88 % Allowed : 18.24 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.42), residues: 417 helix: 2.09 (0.36), residues: 208 sheet: -0.13 (0.72), residues: 63 loop : -1.00 (0.47), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 122 TYR 0.009 0.001 TYR A 363 PHE 0.011 0.001 PHE A 341 TRP 0.007 0.001 TRP A 382 HIS 0.002 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 3399) covalent geometry : angle 0.53681 ( 4617) hydrogen bonds : bond 0.03671 ( 173) hydrogen bonds : angle 3.75915 ( 547) *********************** 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 59 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.162 Fit side-chains REVERT: A 214 LYS cc_start: 0.8938 (mttm) cc_final: 0.8521 (mttp) REVERT: A 297 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8355 (pp) REVERT: A 367 GLU cc_start: 0.8384 (mp0) cc_final: 0.8085 (mp0) REVERT: A 388 HIS cc_start: 0.8845 (OUTLIER) cc_final: 0.7727 (t70) outliers start: 3 outliers final: 1 residues processed: 57 average time/residue: 0.5866 time to fit residues: 34.4053 Evaluate side-chains 59 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 38 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 17 optimal weight: 0.0040 chunk 9 optimal weight: 0.4980 chunk 34 optimal weight: 0.6980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.137021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.092867 restraints weight = 9962.559| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.69 r_work: 0.2811 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2698 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2698 r_free = 0.2698 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2698 r_free = 0.2698 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2698 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 3399 Z= 0.108 Angle : 0.542 8.809 4617 Z= 0.272 Chirality : 0.043 0.157 502 Planarity : 0.005 0.066 589 Dihedral : 5.386 55.755 466 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.88 % Allowed : 17.94 % Favored : 81.18 % 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: 2.26 (0.37), residues: 203 sheet: -0.04 (0.72), residues: 62 loop : -0.96 (0.46), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 58 TYR 0.008 0.001 TYR A 363 PHE 0.011 0.001 PHE A 341 TRP 0.009 0.001 TRP A 382 HIS 0.002 0.000 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 3399) covalent geometry : angle 0.54227 ( 4617) hydrogen bonds : bond 0.03398 ( 173) hydrogen bonds : angle 3.67348 ( 547) ********************** 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 63 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.125 Fit side-chains REVERT: A 9 MET cc_start: 0.8604 (mmp) cc_final: 0.8376 (mmt) REVERT: A 214 LYS cc_start: 0.8975 (mttm) cc_final: 0.8546 (mttp) REVERT: A 297 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.8307 (pp) REVERT: A 367 GLU cc_start: 0.8340 (mp0) cc_final: 0.8049 (mp0) REVERT: A 388 HIS cc_start: 0.8786 (OUTLIER) cc_final: 0.7727 (t70) REVERT: A 392 ASN cc_start: 0.8804 (t0) cc_final: 0.8568 (t0) outliers start: 3 outliers final: 1 residues processed: 61 average time/residue: 0.6187 time to fit residues: 38.8280 Evaluate side-chains 61 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 30 optimal weight: 0.0770 chunk 36 optimal weight: 2.9990 chunk 0 optimal weight: 0.7980 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.135986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.092465 restraints weight = 7363.819| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.32 r_work: 0.2811 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2699 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2699 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3399 Z= 0.116 Angle : 0.575 11.405 4617 Z= 0.282 Chirality : 0.043 0.159 502 Planarity : 0.005 0.058 589 Dihedral : 5.424 55.843 466 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.88 % Allowed : 18.24 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.42), residues: 417 helix: 2.23 (0.37), residues: 203 sheet: -0.04 (0.72), residues: 62 loop : -0.96 (0.45), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 246 TYR 0.010 0.001 TYR A 363 PHE 0.009 0.001 PHE A 341 TRP 0.011 0.001 TRP A 382 HIS 0.002 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 3399) covalent geometry : angle 0.57454 ( 4617) hydrogen bonds : bond 0.03636 ( 173) hydrogen bonds : angle 3.69489 ( 547) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1834.49 seconds wall clock time: 32 minutes 5.33 seconds (1925.33 seconds total)