Starting phenix.real_space_refine on Wed Sep 17 05:13:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ja6_61291/09_2025/9ja6_61291.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ja6_61291/09_2025/9ja6_61291.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ja6_61291/09_2025/9ja6_61291.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ja6_61291/09_2025/9ja6_61291.map" model { file = "/net/cci-nas-00/data/ceres_data/9ja6_61291/09_2025/9ja6_61291.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ja6_61291/09_2025/9ja6_61291.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 3020 2.51 5 N 884 2.21 5 O 948 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s 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: 4880 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1220 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain: "B" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1220 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain: "C" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1220 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain: "D" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1220 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 6, 'TRANS': 140} Time building chain proxies: 1.63, per 1000 atoms: 0.33 Number of scatterers: 4880 At special positions: 0 Unit cell: (92, 92, 120, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 948 8.00 N 884 7.00 C 3020 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: 0.45 Conformation dependent library (CDL) restraints added in 202.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1136 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 0 sheets defined 72.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 208 through 274 removed outlier: 3.811A pdb=" N SER A 274 " --> pdb=" O MET A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 305 removed outlier: 3.672A pdb=" N ILE A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 318 Processing helix chain 'A' and resid 326 through 328 No H-bonds generated for 'chain 'A' and resid 326 through 328' Processing helix chain 'A' and resid 329 through 339 Processing helix chain 'A' and resid 342 through 348 Processing helix chain 'B' and resid 209 through 274 removed outlier: 3.810A pdb=" N SER B 274 " --> pdb=" O MET B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 305 removed outlier: 3.672A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 318 Processing helix chain 'B' and resid 326 through 328 No H-bonds generated for 'chain 'B' and resid 326 through 328' Processing helix chain 'B' and resid 329 through 339 Processing helix chain 'B' and resid 342 through 348 Processing helix chain 'C' and resid 209 through 274 removed outlier: 3.810A pdb=" N SER C 274 " --> pdb=" O MET C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 305 removed outlier: 3.672A pdb=" N ILE C 303 " --> pdb=" O ARG C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 318 Processing helix chain 'C' and resid 326 through 328 No H-bonds generated for 'chain 'C' and resid 326 through 328' Processing helix chain 'C' and resid 329 through 339 Processing helix chain 'C' and resid 342 through 348 Processing helix chain 'D' and resid 209 through 274 removed outlier: 3.810A pdb=" N SER D 274 " --> pdb=" O MET D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 305 removed outlier: 3.672A pdb=" N ILE D 303 " --> pdb=" O ARG D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 318 Processing helix chain 'D' and resid 326 through 328 No H-bonds generated for 'chain 'D' and resid 326 through 328' Processing helix chain 'D' and resid 329 through 339 Processing helix chain 'D' and resid 342 through 348 325 hydrogen bonds defined for protein. 975 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: 0.63 Time building geometry restraints manager: 0.65 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: 1629 1.33 - 1.45: 605 1.45 - 1.57: 2678 1.57 - 1.69: 0 1.69 - 1.80: 52 Bond restraints: 4964 Sorted by residual: bond pdb=" CA GLU A 217 " pdb=" C GLU A 217 " ideal model delta sigma weight residual 1.523 1.480 0.043 1.30e-02 5.92e+03 1.12e+01 bond pdb=" CA ALA C 214 " pdb=" C ALA C 214 " ideal model delta sigma weight residual 1.523 1.480 0.043 1.30e-02 5.92e+03 1.08e+01 bond pdb=" CA ALA B 214 " pdb=" C ALA B 214 " ideal model delta sigma weight residual 1.523 1.482 0.041 1.30e-02 5.92e+03 9.97e+00 bond pdb=" CA ALA A 214 " pdb=" C ALA A 214 " ideal model delta sigma weight residual 1.523 1.482 0.041 1.30e-02 5.92e+03 9.95e+00 bond pdb=" CA ALA D 214 " pdb=" C ALA D 214 " ideal model delta sigma weight residual 1.523 1.483 0.040 1.30e-02 5.92e+03 9.55e+00 ... (remaining 4959 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 6483 2.29 - 4.58: 173 4.58 - 6.87: 21 6.87 - 9.17: 3 9.17 - 11.46: 4 Bond angle restraints: 6684 Sorted by residual: angle pdb=" N ALA C 214 " pdb=" CA ALA C 214 " pdb=" C ALA C 214 " ideal model delta sigma weight residual 111.28 105.93 5.35 1.09e+00 8.42e-01 2.41e+01 angle pdb=" N GLU A 217 " pdb=" CA GLU A 217 " pdb=" C GLU A 217 " ideal model delta sigma weight residual 111.28 106.10 5.18 1.09e+00 8.42e-01 2.26e+01 angle pdb=" N ALA B 214 " pdb=" CA ALA B 214 " pdb=" C ALA B 214 " ideal model delta sigma weight residual 111.28 106.50 4.78 1.09e+00 8.42e-01 1.92e+01 angle pdb=" N ALA A 214 " pdb=" CA ALA A 214 " pdb=" C ALA A 214 " ideal model delta sigma weight residual 111.28 106.54 4.74 1.09e+00 8.42e-01 1.89e+01 angle pdb=" N GLU D 217 " pdb=" CA GLU D 217 " pdb=" C GLU D 217 " ideal model delta sigma weight residual 111.28 107.08 4.20 1.09e+00 8.42e-01 1.48e+01 ... (remaining 6679 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 2662 17.14 - 34.29: 313 34.29 - 51.43: 88 51.43 - 68.58: 29 68.58 - 85.72: 4 Dihedral angle restraints: 3096 sinusoidal: 1356 harmonic: 1740 Sorted by residual: dihedral pdb=" CA ARG C 299 " pdb=" C ARG C 299 " pdb=" N ILE C 300 " pdb=" CA ILE C 300 " ideal model delta harmonic sigma weight residual 180.00 -162.64 -17.36 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA ARG B 299 " pdb=" C ARG B 299 " pdb=" N ILE B 300 " pdb=" CA ILE B 300 " ideal model delta harmonic sigma weight residual -180.00 -162.65 -17.35 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA ARG D 299 " pdb=" C ARG D 299 " pdb=" N ILE D 300 " pdb=" CA ILE D 300 " ideal model delta harmonic sigma weight residual 180.00 -162.67 -17.33 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 3093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 330 0.027 - 0.054: 214 0.054 - 0.082: 128 0.082 - 0.109: 22 0.109 - 0.136: 10 Chirality restraints: 704 Sorted by residual: chirality pdb=" CG LEU D 264 " pdb=" CB LEU D 264 " pdb=" CD1 LEU D 264 " pdb=" CD2 LEU D 264 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.62e-01 chirality pdb=" CG LEU C 264 " pdb=" CB LEU C 264 " pdb=" CD1 LEU C 264 " pdb=" CD2 LEU C 264 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.13 2.00e-01 2.50e+01 4.55e-01 chirality pdb=" CG LEU A 264 " pdb=" CB LEU A 264 " pdb=" CD1 LEU A 264 " pdb=" CD2 LEU A 264 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.51e-01 ... (remaining 701 not shown) Planarity restraints: 888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 216 " -0.010 2.00e-02 2.50e+03 2.08e-02 4.35e+00 pdb=" C GLU C 216 " 0.036 2.00e-02 2.50e+03 pdb=" O GLU C 216 " -0.014 2.00e-02 2.50e+03 pdb=" N GLU C 217 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 216 " 0.009 2.00e-02 2.50e+03 1.85e-02 3.43e+00 pdb=" C GLU A 216 " -0.032 2.00e-02 2.50e+03 pdb=" O GLU A 216 " 0.012 2.00e-02 2.50e+03 pdb=" N GLU A 217 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 213 " -0.008 2.00e-02 2.50e+03 1.65e-02 2.73e+00 pdb=" C LYS B 213 " 0.029 2.00e-02 2.50e+03 pdb=" O LYS B 213 " -0.011 2.00e-02 2.50e+03 pdb=" N ALA B 214 " -0.010 2.00e-02 2.50e+03 ... (remaining 885 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 975 2.75 - 3.29: 5306 3.29 - 3.82: 8175 3.82 - 4.36: 9288 4.36 - 4.90: 13784 Nonbonded interactions: 37528 Sorted by model distance: nonbonded pdb=" OD1 ASP D 304 " pdb=" NZ LYS D 331 " model vdw 2.211 3.120 nonbonded pdb=" OD1 ASP B 304 " pdb=" NZ LYS B 331 " model vdw 2.211 3.120 nonbonded pdb=" OD1 ASP C 304 " pdb=" NZ LYS C 331 " model vdw 2.211 3.120 nonbonded pdb=" OD1 ASP A 304 " pdb=" NZ LYS A 331 " model vdw 2.211 3.120 nonbonded pdb=" OD2 ASP B 304 " pdb=" OH TYR B 348 " model vdw 2.249 3.040 ... (remaining 37523 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.680 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.030 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6396 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 : 0.008 0.047 4964 Z= 0.410 Angle : 0.942 11.457 6684 Z= 0.560 Chirality : 0.043 0.136 704 Planarity : 0.004 0.021 888 Dihedral : 16.510 85.724 1960 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 19.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 9.56 % Allowed : 9.74 % Favored : 80.70 % 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: -1.98 (0.32), residues: 580 helix: -1.17 (0.22), residues: 412 sheet: None (None), residues: 0 loop : -1.24 (0.54), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 222 TYR 0.012 0.002 TYR C 344 PHE 0.010 0.002 PHE C 275 TRP 0.006 0.001 TRP B 221 Details of bonding type rmsd covalent geometry : bond 0.00785 ( 4964) covalent geometry : angle 0.94241 ( 6684) hydrogen bonds : bond 0.09095 ( 325) hydrogen bonds : angle 6.84225 ( 975) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 238 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 GLU cc_start: 0.7273 (mp0) cc_final: 0.6856 (mp0) REVERT: A 270 MET cc_start: 0.8052 (mtp) cc_final: 0.7609 (mtp) REVERT: A 282 VAL cc_start: 0.8598 (OUTLIER) cc_final: 0.8355 (p) REVERT: A 331 LYS cc_start: 0.8465 (mttt) cc_final: 0.8135 (mttt) REVERT: B 220 GLU cc_start: 0.7569 (mp0) cc_final: 0.7185 (mp0) REVERT: B 242 VAL cc_start: 0.8695 (t) cc_final: 0.8396 (t) REVERT: B 260 MET cc_start: 0.5681 (ttp) cc_final: 0.5273 (ttp) REVERT: B 314 TYR cc_start: 0.8369 (OUTLIER) cc_final: 0.8027 (m-10) REVERT: B 325 ASN cc_start: 0.7286 (OUTLIER) cc_final: 0.6694 (p0) REVERT: B 331 LYS cc_start: 0.8148 (mttt) cc_final: 0.7828 (mtpt) REVERT: C 222 ARG cc_start: 0.8634 (mtt-85) cc_final: 0.8282 (mtt-85) REVERT: C 242 VAL cc_start: 0.8918 (t) cc_final: 0.8717 (t) REVERT: C 260 MET cc_start: 0.5597 (ttp) cc_final: 0.5340 (ttp) REVERT: C 270 MET cc_start: 0.8300 (mtp) cc_final: 0.7692 (ttm) REVERT: C 286 ASN cc_start: 0.7916 (p0) cc_final: 0.7650 (p0) REVERT: C 304 ASP cc_start: 0.5186 (t0) cc_final: 0.4412 (t0) REVERT: C 308 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7271 (tm-30) REVERT: C 316 LYS cc_start: 0.8920 (tppp) cc_final: 0.8709 (tppp) REVERT: C 325 ASN cc_start: 0.6600 (OUTLIER) cc_final: 0.6007 (p0) REVERT: C 331 LYS cc_start: 0.8079 (mttt) cc_final: 0.7783 (mttt) REVERT: D 260 MET cc_start: 0.5585 (ttp) cc_final: 0.4938 (ttp) REVERT: D 270 MET cc_start: 0.8373 (mtp) cc_final: 0.7419 (mmm) REVERT: D 286 ASN cc_start: 0.7794 (p0) cc_final: 0.7526 (p0) REVERT: D 304 ASP cc_start: 0.5297 (t0) cc_final: 0.4719 (t0) REVERT: D 314 TYR cc_start: 0.8476 (OUTLIER) cc_final: 0.8047 (m-10) outliers start: 52 outliers final: 18 residues processed: 271 average time/residue: 0.1087 time to fit residues: 35.1708 Evaluate side-chains 250 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 226 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 54 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 0.0170 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 231 ASN C 231 ASN D 231 ASN D 267 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.107497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.089648 restraints weight = 12720.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.093494 restraints weight = 6974.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.096161 restraints weight = 4468.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.098078 restraints weight = 3131.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.099506 restraints weight = 2332.925| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 4964 Z= 0.133 Angle : 0.539 7.017 6684 Z= 0.297 Chirality : 0.039 0.149 704 Planarity : 0.005 0.045 888 Dihedral : 4.030 17.835 668 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.18 % Allowed : 4.04 % Favored : 95.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.67 (0.35), residues: 580 helix: 1.66 (0.24), residues: 412 sheet: None (None), residues: 0 loop : -0.18 (0.54), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 222 TYR 0.009 0.001 TYR B 314 PHE 0.008 0.001 PHE C 284 TRP 0.012 0.002 TRP B 330 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 4964) covalent geometry : angle 0.53944 ( 6684) hydrogen bonds : bond 0.04615 ( 325) hydrogen bonds : angle 4.19774 ( 975) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 223 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 LYS cc_start: 0.8967 (mttt) cc_final: 0.8688 (mttt) REVERT: A 217 GLU cc_start: 0.7455 (pp20) cc_final: 0.7161 (pp20) REVERT: A 222 ARG cc_start: 0.8619 (mtt-85) cc_final: 0.7661 (mtp85) REVERT: A 227 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7725 (mm-30) REVERT: A 262 MET cc_start: 0.7790 (tmm) cc_final: 0.7389 (tmm) REVERT: A 270 MET cc_start: 0.7731 (mtp) cc_final: 0.7474 (mtp) REVERT: A 272 MET cc_start: 0.8486 (mmt) cc_final: 0.8176 (mmt) REVERT: A 275 PHE cc_start: 0.8689 (m-80) cc_final: 0.8258 (m-80) REVERT: A 282 VAL cc_start: 0.8808 (t) cc_final: 0.8494 (p) REVERT: A 299 ARG cc_start: 0.8084 (ttm170) cc_final: 0.7657 (ttm170) REVERT: A 316 LYS cc_start: 0.8795 (tppp) cc_final: 0.8368 (mttt) REVERT: B 208 MET cc_start: 0.8192 (mmm) cc_final: 0.7652 (mmm) REVERT: B 222 ARG cc_start: 0.8885 (mtt-85) cc_final: 0.8573 (mtt-85) REVERT: B 227 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8330 (mm-30) REVERT: B 246 MET cc_start: 0.9081 (mtp) cc_final: 0.8558 (mtp) REVERT: B 268 ASN cc_start: 0.8457 (m-40) cc_final: 0.8216 (m-40) REVERT: B 275 PHE cc_start: 0.8836 (m-80) cc_final: 0.8208 (m-80) REVERT: B 299 ARG cc_start: 0.8230 (ttm170) cc_final: 0.7868 (ttm170) REVERT: B 316 LYS cc_start: 0.8718 (mmtp) cc_final: 0.8235 (mmtp) REVERT: B 331 LYS cc_start: 0.9003 (mttt) cc_final: 0.8618 (mttt) REVERT: B 344 TYR cc_start: 0.8479 (t80) cc_final: 0.8248 (t80) REVERT: C 211 TRP cc_start: 0.8610 (m100) cc_final: 0.8107 (m100) REVERT: C 212 LYS cc_start: 0.9193 (mttt) cc_final: 0.8877 (mmmt) REVERT: C 217 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8106 (mt-10) REVERT: C 222 ARG cc_start: 0.9033 (mtt-85) cc_final: 0.8394 (mtt-85) REVERT: C 226 ASP cc_start: 0.8557 (t0) cc_final: 0.8330 (t0) REVERT: C 227 GLU cc_start: 0.8958 (mm-30) cc_final: 0.8574 (mm-30) REVERT: C 246 MET cc_start: 0.8818 (mtp) cc_final: 0.8381 (mtp) REVERT: C 248 ASN cc_start: 0.9096 (m-40) cc_final: 0.8892 (m-40) REVERT: C 249 ASP cc_start: 0.8773 (t70) cc_final: 0.8477 (t70) REVERT: C 262 MET cc_start: 0.8053 (tmm) cc_final: 0.7220 (tmm) REVERT: C 275 PHE cc_start: 0.8772 (m-80) cc_final: 0.8251 (m-80) REVERT: C 299 ARG cc_start: 0.8377 (ptp-110) cc_final: 0.8129 (ttp-110) REVERT: C 316 LYS cc_start: 0.8840 (tppp) cc_final: 0.8533 (tppp) REVERT: C 325 ASN cc_start: 0.7117 (m-40) cc_final: 0.6879 (p0) REVERT: C 344 TYR cc_start: 0.8635 (t80) cc_final: 0.8244 (t80) REVERT: D 212 LYS cc_start: 0.8728 (mmtm) cc_final: 0.8472 (mmmt) REVERT: D 245 ASP cc_start: 0.8855 (m-30) cc_final: 0.8576 (m-30) REVERT: D 262 MET cc_start: 0.8104 (tmm) cc_final: 0.7770 (tmm) REVERT: D 269 ASN cc_start: 0.9296 (m-40) cc_final: 0.9089 (m-40) REVERT: D 282 VAL cc_start: 0.8777 (t) cc_final: 0.8563 (p) outliers start: 1 outliers final: 0 residues processed: 224 average time/residue: 0.1076 time to fit residues: 28.8424 Evaluate side-chains 211 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 37 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 22 optimal weight: 0.1980 chunk 23 optimal weight: 0.6980 chunk 6 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 GLN A 269 ASN A 310 ASN B 243 GLN C 243 GLN C 327 GLN D 243 GLN D 268 ASN D 327 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.101205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.085457 restraints weight = 12507.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.089143 restraints weight = 6660.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.091711 restraints weight = 4200.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.093509 restraints weight = 2894.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.094893 restraints weight = 2103.895| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.5127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4964 Z= 0.133 Angle : 0.516 6.226 6684 Z= 0.294 Chirality : 0.038 0.134 704 Planarity : 0.004 0.040 888 Dihedral : 3.749 17.048 668 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 0.18 % Allowed : 1.47 % Favored : 98.35 % 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: 2.64 (0.36), residues: 580 helix: 2.40 (0.24), residues: 412 sheet: None (None), residues: 0 loop : 0.13 (0.56), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 255 TYR 0.007 0.001 TYR B 314 PHE 0.010 0.001 PHE A 284 TRP 0.017 0.002 TRP D 211 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 4964) covalent geometry : angle 0.51605 ( 6684) hydrogen bonds : bond 0.04273 ( 325) hydrogen bonds : angle 3.92788 ( 975) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 217 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 LYS cc_start: 0.9039 (mttt) cc_final: 0.8740 (mttt) REVERT: A 217 GLU cc_start: 0.7540 (pp20) cc_final: 0.7337 (pp20) REVERT: A 222 ARG cc_start: 0.8622 (mtt-85) cc_final: 0.8100 (mtt-85) REVERT: A 242 VAL cc_start: 0.9261 (p) cc_final: 0.9012 (p) REVERT: A 247 ARG cc_start: 0.9104 (ttm170) cc_final: 0.8802 (ttm170) REVERT: A 262 MET cc_start: 0.7910 (tmm) cc_final: 0.7280 (tmm) REVERT: A 265 SER cc_start: 0.8818 (m) cc_final: 0.8603 (p) REVERT: A 270 MET cc_start: 0.7970 (mtp) cc_final: 0.7693 (mtp) REVERT: A 275 PHE cc_start: 0.8727 (m-80) cc_final: 0.8274 (m-80) REVERT: A 282 VAL cc_start: 0.8811 (t) cc_final: 0.8449 (p) REVERT: A 299 ARG cc_start: 0.8105 (ttm170) cc_final: 0.7690 (ttm170) REVERT: A 316 LYS cc_start: 0.8880 (tppp) cc_final: 0.8451 (mttt) REVERT: A 344 TYR cc_start: 0.8037 (t80) cc_final: 0.7822 (t80) REVERT: B 208 MET cc_start: 0.8159 (mmm) cc_final: 0.7290 (mmm) REVERT: B 211 TRP cc_start: 0.8416 (m100) cc_final: 0.7442 (m100) REVERT: B 222 ARG cc_start: 0.8866 (mtt-85) cc_final: 0.8243 (mtt-85) REVERT: B 227 GLU cc_start: 0.8781 (mm-30) cc_final: 0.8351 (mm-30) REVERT: B 246 MET cc_start: 0.9115 (mtp) cc_final: 0.8584 (mtp) REVERT: B 268 ASN cc_start: 0.8388 (m-40) cc_final: 0.8099 (m-40) REVERT: B 275 PHE cc_start: 0.8788 (m-80) cc_final: 0.8180 (m-80) REVERT: B 316 LYS cc_start: 0.8734 (mmtp) cc_final: 0.8222 (mmtp) REVERT: B 322 TYR cc_start: 0.6116 (p90) cc_final: 0.5764 (p90) REVERT: B 331 LYS cc_start: 0.8984 (mttt) cc_final: 0.8350 (mttt) REVERT: B 332 ARG cc_start: 0.8286 (mmt180) cc_final: 0.8083 (mmt-90) REVERT: B 344 TYR cc_start: 0.8496 (t80) cc_final: 0.8246 (t80) REVERT: B 348 TYR cc_start: 0.8041 (t80) cc_final: 0.7700 (t80) REVERT: C 211 TRP cc_start: 0.8465 (m100) cc_final: 0.7756 (m100) REVERT: C 212 LYS cc_start: 0.9253 (mttt) cc_final: 0.8918 (mmmt) REVERT: C 217 GLU cc_start: 0.8342 (mt-10) cc_final: 0.8052 (mt-10) REVERT: C 222 ARG cc_start: 0.9027 (mtt-85) cc_final: 0.8466 (mtt-85) REVERT: C 226 ASP cc_start: 0.8619 (t0) cc_final: 0.8416 (t0) REVERT: C 227 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8542 (mm-30) REVERT: C 246 MET cc_start: 0.9077 (mtp) cc_final: 0.8690 (mtp) REVERT: C 249 ASP cc_start: 0.8763 (t70) cc_final: 0.8382 (t70) REVERT: C 262 MET cc_start: 0.7904 (tmm) cc_final: 0.7091 (tmm) REVERT: C 270 MET cc_start: 0.8463 (ttm) cc_final: 0.7637 (tpt) REVERT: C 275 PHE cc_start: 0.8814 (m-80) cc_final: 0.8207 (m-80) REVERT: C 282 VAL cc_start: 0.8501 (t) cc_final: 0.7291 (t) REVERT: C 295 PRO cc_start: 0.8110 (Cg_exo) cc_final: 0.7846 (Cg_endo) REVERT: C 296 ARG cc_start: 0.8340 (mmt180) cc_final: 0.7585 (mmt180) REVERT: C 297 ILE cc_start: 0.8146 (mm) cc_final: 0.7862 (mm) REVERT: C 316 LYS cc_start: 0.8793 (tppp) cc_final: 0.8431 (tppp) REVERT: C 331 LYS cc_start: 0.9012 (mtpt) cc_final: 0.8576 (mttt) REVERT: C 344 TYR cc_start: 0.8543 (t80) cc_final: 0.8136 (t80) REVERT: C 348 TYR cc_start: 0.7977 (t80) cc_final: 0.7622 (t80) REVERT: D 212 LYS cc_start: 0.8832 (mmtm) cc_final: 0.8586 (mmmt) REVERT: D 244 ARG cc_start: 0.8859 (ttm170) cc_final: 0.8553 (ttm170) REVERT: D 245 ASP cc_start: 0.8893 (m-30) cc_final: 0.8612 (m-30) REVERT: D 246 MET cc_start: 0.8821 (ptp) cc_final: 0.8545 (ptp) REVERT: D 257 VAL cc_start: 0.8897 (t) cc_final: 0.8593 (t) REVERT: D 262 MET cc_start: 0.8022 (tmm) cc_final: 0.7603 (tmm) REVERT: D 275 PHE cc_start: 0.8856 (m-10) cc_final: 0.8378 (m-10) REVERT: D 282 VAL cc_start: 0.8717 (t) cc_final: 0.8461 (p) REVERT: D 309 GLU cc_start: 0.8560 (pp20) cc_final: 0.8139 (pp20) REVERT: D 313 ARG cc_start: 0.8941 (mmp80) cc_final: 0.8528 (mmp80) REVERT: D 316 LYS cc_start: 0.8537 (mmmm) cc_final: 0.7767 (mmmm) REVERT: D 331 LYS cc_start: 0.8946 (mtpt) cc_final: 0.8138 (tttt) REVERT: D 344 TYR cc_start: 0.8640 (t80) cc_final: 0.8177 (t80) outliers start: 1 outliers final: 1 residues processed: 217 average time/residue: 0.1215 time to fit residues: 31.0259 Evaluate side-chains 217 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 216 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 31 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN B 231 ASN B 269 ASN B 310 ASN C 310 ASN C 327 GLN D 267 ASN D 268 ASN D 327 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.099286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.084362 restraints weight = 12951.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.087951 restraints weight = 6601.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.090378 restraints weight = 4043.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.091987 restraints weight = 2728.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.093257 restraints weight = 1982.048| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.6173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4964 Z= 0.167 Angle : 0.521 7.002 6684 Z= 0.300 Chirality : 0.039 0.139 704 Planarity : 0.004 0.035 888 Dihedral : 3.903 21.312 668 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % 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: 2.84 (0.36), residues: 580 helix: 2.50 (0.24), residues: 412 sheet: None (None), residues: 0 loop : 0.36 (0.58), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 215 TYR 0.012 0.001 TYR C 314 PHE 0.004 0.001 PHE B 350 TRP 0.024 0.003 TRP D 211 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 4964) covalent geometry : angle 0.52145 ( 6684) hydrogen bonds : bond 0.04149 ( 325) hydrogen bonds : angle 4.07344 ( 975) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ARG cc_start: 0.8785 (mtt-85) cc_final: 0.8256 (mtt-85) REVERT: A 227 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8436 (mm-30) REVERT: A 242 VAL cc_start: 0.9288 (p) cc_final: 0.9023 (p) REVERT: A 262 MET cc_start: 0.8125 (tmm) cc_final: 0.7672 (tmm) REVERT: A 270 MET cc_start: 0.7846 (mtp) cc_final: 0.7492 (mtp) REVERT: A 272 MET cc_start: 0.8256 (mmt) cc_final: 0.7700 (mmt) REVERT: A 275 PHE cc_start: 0.8796 (m-80) cc_final: 0.8258 (m-80) REVERT: A 282 VAL cc_start: 0.8544 (t) cc_final: 0.8264 (p) REVERT: A 299 ARG cc_start: 0.8185 (ttm170) cc_final: 0.7827 (ttm170) REVERT: A 316 LYS cc_start: 0.8650 (tppp) cc_final: 0.8322 (tppp) REVERT: A 344 TYR cc_start: 0.8141 (t80) cc_final: 0.7888 (t80) REVERT: B 208 MET cc_start: 0.8601 (mmm) cc_final: 0.8310 (mmm) REVERT: B 211 TRP cc_start: 0.8777 (m100) cc_final: 0.7941 (m100) REVERT: B 213 LYS cc_start: 0.8833 (mtmm) cc_final: 0.8609 (mtmm) REVERT: B 222 ARG cc_start: 0.8973 (mtt-85) cc_final: 0.8403 (mtt-85) REVERT: B 228 ARG cc_start: 0.9209 (mtt180) cc_final: 0.8885 (mtt180) REVERT: B 268 ASN cc_start: 0.8679 (m-40) cc_final: 0.8451 (m-40) REVERT: B 275 PHE cc_start: 0.8735 (m-80) cc_final: 0.8215 (m-80) REVERT: B 299 ARG cc_start: 0.8202 (ttm170) cc_final: 0.7834 (ttm170) REVERT: B 310 ASN cc_start: 0.8848 (m110) cc_final: 0.8574 (p0) REVERT: B 316 LYS cc_start: 0.8386 (mmtp) cc_final: 0.7900 (mmtp) REVERT: B 344 TYR cc_start: 0.8460 (t80) cc_final: 0.8234 (t80) REVERT: B 348 TYR cc_start: 0.7701 (t80) cc_final: 0.7274 (t80) REVERT: C 212 LYS cc_start: 0.9179 (mttt) cc_final: 0.8932 (mmmt) REVERT: C 217 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8217 (mt-10) REVERT: C 218 ASP cc_start: 0.8478 (m-30) cc_final: 0.8195 (m-30) REVERT: C 228 ARG cc_start: 0.9081 (mtt180) cc_final: 0.8752 (mtt180) REVERT: C 246 MET cc_start: 0.9080 (mtp) cc_final: 0.8700 (mtp) REVERT: C 249 ASP cc_start: 0.8831 (t70) cc_final: 0.8513 (t70) REVERT: C 262 MET cc_start: 0.7897 (tmm) cc_final: 0.7178 (tmm) REVERT: C 275 PHE cc_start: 0.8788 (m-80) cc_final: 0.8281 (m-80) REVERT: C 282 VAL cc_start: 0.8128 (t) cc_final: 0.6609 (t) REVERT: C 296 ARG cc_start: 0.8232 (mmt180) cc_final: 0.7329 (mmt180) REVERT: C 299 ARG cc_start: 0.8536 (ptp-170) cc_final: 0.8280 (ttp-110) REVERT: C 316 LYS cc_start: 0.8502 (tppp) cc_final: 0.8210 (tppp) REVERT: C 331 LYS cc_start: 0.8864 (mtpt) cc_final: 0.8010 (ttmt) REVERT: C 344 TYR cc_start: 0.8534 (t80) cc_final: 0.8177 (t80) REVERT: C 348 TYR cc_start: 0.7570 (t80) cc_final: 0.7156 (t80) REVERT: D 218 ASP cc_start: 0.8191 (m-30) cc_final: 0.7902 (m-30) REVERT: D 242 VAL cc_start: 0.9025 (t) cc_final: 0.8775 (t) REVERT: D 245 ASP cc_start: 0.8824 (m-30) cc_final: 0.8579 (m-30) REVERT: D 246 MET cc_start: 0.8851 (ptp) cc_final: 0.8549 (ptp) REVERT: D 257 VAL cc_start: 0.8840 (t) cc_final: 0.8632 (t) REVERT: D 262 MET cc_start: 0.8032 (tmm) cc_final: 0.7682 (tmm) REVERT: D 268 ASN cc_start: 0.8556 (m-40) cc_final: 0.8335 (m-40) REVERT: D 270 MET cc_start: 0.8390 (ttm) cc_final: 0.8099 (ttm) REVERT: D 275 PHE cc_start: 0.8808 (m-10) cc_final: 0.8394 (m-10) REVERT: D 281 GLU cc_start: 0.7770 (tt0) cc_final: 0.7518 (tt0) REVERT: D 304 ASP cc_start: 0.6879 (t0) cc_final: 0.6029 (t0) REVERT: D 309 GLU cc_start: 0.8604 (pp20) cc_final: 0.8211 (pp20) REVERT: D 313 ARG cc_start: 0.8851 (mmp80) cc_final: 0.8505 (mmp80) REVERT: D 316 LYS cc_start: 0.8176 (mmmm) cc_final: 0.7509 (mmmm) REVERT: D 331 LYS cc_start: 0.8744 (mtpt) cc_final: 0.7989 (tttt) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.1217 time to fit residues: 31.3645 Evaluate side-chains 218 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 54 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 50 optimal weight: 0.0270 chunk 32 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 231 ASN B 252 ASN D 231 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.097414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.082198 restraints weight = 12986.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.085844 restraints weight = 6597.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.088373 restraints weight = 4028.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.090048 restraints weight = 2696.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.091266 restraints weight = 1967.383| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.6530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 4964 Z= 0.119 Angle : 0.483 6.011 6684 Z= 0.277 Chirality : 0.038 0.133 704 Planarity : 0.004 0.029 888 Dihedral : 3.659 16.263 668 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % 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: 3.26 (0.36), residues: 580 helix: 2.84 (0.24), residues: 412 sheet: None (None), residues: 0 loop : 0.41 (0.56), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 255 TYR 0.011 0.001 TYR A 314 PHE 0.009 0.001 PHE C 284 TRP 0.013 0.002 TRP C 330 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 4964) covalent geometry : angle 0.48345 ( 6684) hydrogen bonds : bond 0.03857 ( 325) hydrogen bonds : angle 3.83266 ( 975) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 LYS cc_start: 0.9121 (mttt) cc_final: 0.8746 (mttt) REVERT: A 222 ARG cc_start: 0.8625 (mtt-85) cc_final: 0.8228 (mtt-85) REVERT: A 227 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8333 (mm-30) REVERT: A 242 VAL cc_start: 0.9313 (p) cc_final: 0.8984 (p) REVERT: A 262 MET cc_start: 0.8032 (tmm) cc_final: 0.7456 (tmm) REVERT: A 270 MET cc_start: 0.8178 (mtp) cc_final: 0.7906 (mtp) REVERT: A 272 MET cc_start: 0.8228 (mmt) cc_final: 0.7715 (mmt) REVERT: A 275 PHE cc_start: 0.8739 (m-80) cc_final: 0.8264 (m-80) REVERT: A 299 ARG cc_start: 0.7954 (ttm170) cc_final: 0.7639 (ttm170) REVERT: A 316 LYS cc_start: 0.8921 (tppp) cc_final: 0.8514 (tppp) REVERT: A 344 TYR cc_start: 0.8110 (t80) cc_final: 0.7825 (t80) REVERT: B 208 MET cc_start: 0.8101 (mmm) cc_final: 0.7605 (mmm) REVERT: B 211 TRP cc_start: 0.8320 (m100) cc_final: 0.7597 (m100) REVERT: B 217 GLU cc_start: 0.7641 (pp20) cc_final: 0.7192 (pp20) REVERT: B 218 ASP cc_start: 0.7921 (m-30) cc_final: 0.6716 (m-30) REVERT: B 222 ARG cc_start: 0.8793 (mtt-85) cc_final: 0.8246 (mtt-85) REVERT: B 249 ASP cc_start: 0.8612 (t70) cc_final: 0.8157 (t0) REVERT: B 268 ASN cc_start: 0.8444 (m-40) cc_final: 0.8191 (m-40) REVERT: B 275 PHE cc_start: 0.8703 (m-80) cc_final: 0.8174 (m-80) REVERT: B 299 ARG cc_start: 0.7921 (ttm170) cc_final: 0.7610 (ttm170) REVERT: B 316 LYS cc_start: 0.8650 (mmtp) cc_final: 0.7948 (mmtp) REVERT: B 322 TYR cc_start: 0.6713 (p90) cc_final: 0.5997 (p90) REVERT: B 344 TYR cc_start: 0.8443 (t80) cc_final: 0.8161 (t80) REVERT: C 212 LYS cc_start: 0.9334 (mttt) cc_final: 0.9059 (mmmt) REVERT: C 217 GLU cc_start: 0.8381 (mt-10) cc_final: 0.8009 (mt-10) REVERT: C 218 ASP cc_start: 0.8219 (m-30) cc_final: 0.7184 (m-30) REVERT: C 222 ARG cc_start: 0.8953 (mtt-85) cc_final: 0.8432 (mtt-85) REVERT: C 229 LEU cc_start: 0.9178 (mt) cc_final: 0.8941 (mt) REVERT: C 242 VAL cc_start: 0.9069 (t) cc_final: 0.8803 (t) REVERT: C 244 ARG cc_start: 0.8684 (ttm110) cc_final: 0.8267 (ttm110) REVERT: C 246 MET cc_start: 0.8904 (mtp) cc_final: 0.8485 (mtp) REVERT: C 249 ASP cc_start: 0.8580 (t70) cc_final: 0.8143 (t70) REVERT: C 250 LEU cc_start: 0.8654 (tp) cc_final: 0.8327 (tp) REVERT: C 257 VAL cc_start: 0.9096 (t) cc_final: 0.8885 (t) REVERT: C 262 MET cc_start: 0.7912 (tmm) cc_final: 0.7087 (tmm) REVERT: C 272 MET cc_start: 0.7875 (mmt) cc_final: 0.7337 (mmt) REVERT: C 275 PHE cc_start: 0.8802 (m-80) cc_final: 0.8241 (m-80) REVERT: C 282 VAL cc_start: 0.8691 (t) cc_final: 0.7705 (t) REVERT: C 296 ARG cc_start: 0.8147 (mmt180) cc_final: 0.7380 (mmt180) REVERT: C 313 ARG cc_start: 0.8997 (mtp85) cc_final: 0.8616 (mtp85) REVERT: C 316 LYS cc_start: 0.8752 (tppp) cc_final: 0.8255 (tppp) REVERT: C 322 TYR cc_start: 0.6920 (p90) cc_final: 0.6670 (p90) REVERT: C 331 LYS cc_start: 0.9095 (mtpt) cc_final: 0.8112 (ttmt) REVERT: C 344 TYR cc_start: 0.8506 (t80) cc_final: 0.8121 (t80) REVERT: C 348 TYR cc_start: 0.8183 (t80) cc_final: 0.7892 (t80) REVERT: D 218 ASP cc_start: 0.7819 (m-30) cc_final: 0.7355 (m-30) REVERT: D 242 VAL cc_start: 0.8998 (t) cc_final: 0.8736 (t) REVERT: D 244 ARG cc_start: 0.8767 (ttm170) cc_final: 0.8415 (ttm170) REVERT: D 245 ASP cc_start: 0.8885 (m-30) cc_final: 0.8572 (m-30) REVERT: D 246 MET cc_start: 0.8548 (ptp) cc_final: 0.8339 (ptp) REVERT: D 249 ASP cc_start: 0.8550 (t70) cc_final: 0.8015 (t70) REVERT: D 262 MET cc_start: 0.7845 (tmm) cc_final: 0.7428 (tmm) REVERT: D 275 PHE cc_start: 0.8753 (m-10) cc_final: 0.8345 (m-10) REVERT: D 281 GLU cc_start: 0.7888 (tt0) cc_final: 0.7618 (tt0) REVERT: D 304 ASP cc_start: 0.6925 (t0) cc_final: 0.6039 (t0) REVERT: D 309 GLU cc_start: 0.8678 (pp20) cc_final: 0.8190 (pp20) REVERT: D 313 ARG cc_start: 0.8921 (mmp80) cc_final: 0.8474 (mmp80) REVERT: D 316 LYS cc_start: 0.8573 (mmmm) cc_final: 0.7737 (mmmm) REVERT: D 331 LYS cc_start: 0.8952 (mtpt) cc_final: 0.8164 (tttt) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.1235 time to fit residues: 31.1630 Evaluate side-chains 215 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 54 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 20 optimal weight: 0.0020 chunk 17 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 ASN B 231 ASN C 231 ASN ** D 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.098426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.083200 restraints weight = 12920.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.086874 restraints weight = 6642.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.089275 restraints weight = 4062.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.091059 restraints weight = 2800.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.092449 restraints weight = 2016.871| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.6892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 4964 Z= 0.116 Angle : 0.494 4.722 6684 Z= 0.283 Chirality : 0.039 0.132 704 Planarity : 0.003 0.026 888 Dihedral : 3.622 18.624 668 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % 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: 3.34 (0.35), residues: 580 helix: 2.95 (0.24), residues: 412 sheet: None (None), residues: 0 loop : 0.31 (0.55), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 255 TYR 0.009 0.001 TYR C 314 PHE 0.005 0.001 PHE B 284 TRP 0.019 0.002 TRP D 211 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 4964) covalent geometry : angle 0.49392 ( 6684) hydrogen bonds : bond 0.03735 ( 325) hydrogen bonds : angle 3.78822 ( 975) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 TRP cc_start: 0.8147 (m100) cc_final: 0.7148 (m100) REVERT: A 213 LYS cc_start: 0.9114 (mttt) cc_final: 0.8732 (mttt) REVERT: A 222 ARG cc_start: 0.8652 (mtt-85) cc_final: 0.8293 (mtt-85) REVERT: A 242 VAL cc_start: 0.9317 (p) cc_final: 0.8977 (p) REVERT: A 262 MET cc_start: 0.8048 (tmm) cc_final: 0.7478 (tmm) REVERT: A 270 MET cc_start: 0.8199 (mtp) cc_final: 0.7883 (mtp) REVERT: A 272 MET cc_start: 0.8223 (mmt) cc_final: 0.7917 (mmt) REVERT: A 275 PHE cc_start: 0.8726 (m-80) cc_final: 0.8276 (m-80) REVERT: A 299 ARG cc_start: 0.7939 (ttm170) cc_final: 0.7631 (ttm170) REVERT: A 316 LYS cc_start: 0.8871 (tppp) cc_final: 0.8451 (tppp) REVERT: A 344 TYR cc_start: 0.8100 (t80) cc_final: 0.7797 (t80) REVERT: B 208 MET cc_start: 0.8120 (mmm) cc_final: 0.7673 (mmm) REVERT: B 211 TRP cc_start: 0.8309 (m100) cc_final: 0.7636 (m100) REVERT: B 217 GLU cc_start: 0.7549 (pp20) cc_final: 0.7097 (pp20) REVERT: B 218 ASP cc_start: 0.7926 (m-30) cc_final: 0.6669 (m-30) REVERT: B 222 ARG cc_start: 0.8748 (mtt-85) cc_final: 0.8236 (mtt-85) REVERT: B 246 MET cc_start: 0.8944 (mtp) cc_final: 0.8585 (mtp) REVERT: B 249 ASP cc_start: 0.8658 (t70) cc_final: 0.8187 (t0) REVERT: B 267 ASN cc_start: 0.7808 (t0) cc_final: 0.7588 (t0) REVERT: B 272 MET cc_start: 0.7860 (mmt) cc_final: 0.7348 (mmt) REVERT: B 275 PHE cc_start: 0.8670 (m-80) cc_final: 0.8161 (m-80) REVERT: B 299 ARG cc_start: 0.7821 (ttm170) cc_final: 0.7534 (ttm170) REVERT: B 316 LYS cc_start: 0.8633 (mmtp) cc_final: 0.7838 (mmtp) REVERT: B 322 TYR cc_start: 0.6669 (p90) cc_final: 0.6381 (p90) REVERT: B 331 LYS cc_start: 0.9120 (mttt) cc_final: 0.8132 (ttmt) REVERT: B 344 TYR cc_start: 0.8437 (t80) cc_final: 0.8054 (t80) REVERT: C 212 LYS cc_start: 0.9335 (mttt) cc_final: 0.9071 (mmmt) REVERT: C 217 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8058 (mt-10) REVERT: C 218 ASP cc_start: 0.8290 (m-30) cc_final: 0.7187 (m-30) REVERT: C 222 ARG cc_start: 0.8968 (mtt-85) cc_final: 0.8402 (mtt-85) REVERT: C 242 VAL cc_start: 0.9086 (t) cc_final: 0.8824 (t) REVERT: C 244 ARG cc_start: 0.8705 (ttm110) cc_final: 0.8270 (ttm110) REVERT: C 246 MET cc_start: 0.8921 (mtp) cc_final: 0.8514 (mtp) REVERT: C 249 ASP cc_start: 0.8604 (t70) cc_final: 0.8161 (t70) REVERT: C 257 VAL cc_start: 0.9090 (t) cc_final: 0.8797 (t) REVERT: C 262 MET cc_start: 0.7897 (tmm) cc_final: 0.7113 (tmm) REVERT: C 270 MET cc_start: 0.8336 (ttm) cc_final: 0.8041 (mmm) REVERT: C 272 MET cc_start: 0.7831 (mmt) cc_final: 0.7405 (mmt) REVERT: C 275 PHE cc_start: 0.8793 (m-80) cc_final: 0.8265 (m-80) REVERT: C 282 VAL cc_start: 0.8733 (t) cc_final: 0.7823 (t) REVERT: C 296 ARG cc_start: 0.8192 (mmt180) cc_final: 0.7308 (mmt180) REVERT: C 313 ARG cc_start: 0.9028 (mtp85) cc_final: 0.8686 (mtp85) REVERT: C 316 LYS cc_start: 0.8709 (tppp) cc_final: 0.8188 (tppp) REVERT: C 322 TYR cc_start: 0.6966 (p90) cc_final: 0.6582 (p90) REVERT: C 331 LYS cc_start: 0.9092 (mtpt) cc_final: 0.8159 (ttmt) REVERT: C 344 TYR cc_start: 0.8492 (t80) cc_final: 0.8070 (t80) REVERT: D 212 LYS cc_start: 0.9017 (mmtm) cc_final: 0.8662 (mmmt) REVERT: D 222 ARG cc_start: 0.8790 (ptp-170) cc_final: 0.8479 (ptp-170) REVERT: D 242 VAL cc_start: 0.9036 (t) cc_final: 0.8770 (t) REVERT: D 245 ASP cc_start: 0.8900 (m-30) cc_final: 0.8605 (m-30) REVERT: D 262 MET cc_start: 0.7800 (tmm) cc_final: 0.7353 (tmm) REVERT: D 270 MET cc_start: 0.8442 (ttm) cc_final: 0.8217 (tpt) REVERT: D 275 PHE cc_start: 0.8737 (m-10) cc_final: 0.8382 (m-10) REVERT: D 281 GLU cc_start: 0.7885 (tt0) cc_final: 0.7582 (tt0) REVERT: D 316 LYS cc_start: 0.8545 (mmmm) cc_final: 0.7831 (mmmm) REVERT: D 331 LYS cc_start: 0.9022 (mtpt) cc_final: 0.8215 (tttt) REVERT: D 332 ARG cc_start: 0.8513 (mmt-90) cc_final: 0.8288 (mmt-90) REVERT: D 344 TYR cc_start: 0.8580 (t80) cc_final: 0.8123 (t80) REVERT: D 348 TYR cc_start: 0.8144 (t80) cc_final: 0.7788 (t80) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.1198 time to fit residues: 29.5930 Evaluate side-chains 207 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 48 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 35 optimal weight: 0.0870 chunk 16 optimal weight: 0.0980 chunk 11 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 ASN A 267 ASN A 310 ASN B 231 ASN C 333 GLN ** D 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.097634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.082476 restraints weight = 12859.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.086181 restraints weight = 6557.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.088807 restraints weight = 4012.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.090594 restraints weight = 2663.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.091883 restraints weight = 1907.064| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.7121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 4964 Z= 0.108 Angle : 0.492 5.930 6684 Z= 0.282 Chirality : 0.039 0.132 704 Planarity : 0.003 0.026 888 Dihedral : 3.578 21.780 668 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % 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: 3.42 (0.35), residues: 580 helix: 3.02 (0.24), residues: 412 sheet: None (None), residues: 0 loop : 0.30 (0.54), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 299 TYR 0.011 0.001 TYR A 314 PHE 0.006 0.001 PHE C 350 TRP 0.016 0.001 TRP D 211 Details of bonding type rmsd covalent geometry : bond 0.00206 ( 4964) covalent geometry : angle 0.49172 ( 6684) hydrogen bonds : bond 0.03608 ( 325) hydrogen bonds : angle 3.79397 ( 975) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 TRP cc_start: 0.8130 (m100) cc_final: 0.7238 (m100) REVERT: A 213 LYS cc_start: 0.9131 (mttt) cc_final: 0.8751 (mttt) REVERT: A 222 ARG cc_start: 0.8650 (mtt-85) cc_final: 0.8291 (mtt-85) REVERT: A 227 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8294 (mm-30) REVERT: A 242 VAL cc_start: 0.9321 (p) cc_final: 0.9002 (p) REVERT: A 262 MET cc_start: 0.8021 (tmm) cc_final: 0.7433 (tmm) REVERT: A 270 MET cc_start: 0.8039 (mtp) cc_final: 0.7742 (mtp) REVERT: A 272 MET cc_start: 0.8221 (mmt) cc_final: 0.7849 (mmt) REVERT: A 275 PHE cc_start: 0.8716 (m-80) cc_final: 0.8304 (m-80) REVERT: A 299 ARG cc_start: 0.7936 (ttm170) cc_final: 0.7650 (ttm170) REVERT: A 316 LYS cc_start: 0.8826 (tppp) cc_final: 0.8396 (tppp) REVERT: A 344 TYR cc_start: 0.8107 (t80) cc_final: 0.7706 (t80) REVERT: A 348 TYR cc_start: 0.7761 (t80) cc_final: 0.7514 (t80) REVERT: B 208 MET cc_start: 0.8055 (mmm) cc_final: 0.7614 (mmm) REVERT: B 211 TRP cc_start: 0.8292 (m100) cc_final: 0.7661 (m100) REVERT: B 222 ARG cc_start: 0.8746 (mtt-85) cc_final: 0.8235 (mtt-85) REVERT: B 246 MET cc_start: 0.8915 (mtp) cc_final: 0.8579 (mtp) REVERT: B 272 MET cc_start: 0.7779 (mmt) cc_final: 0.7337 (mmt) REVERT: B 275 PHE cc_start: 0.8652 (m-80) cc_final: 0.8154 (m-80) REVERT: B 299 ARG cc_start: 0.7794 (ttm170) cc_final: 0.7481 (ttm170) REVERT: B 316 LYS cc_start: 0.8606 (mmtp) cc_final: 0.7876 (mmtp) REVERT: B 322 TYR cc_start: 0.6717 (p90) cc_final: 0.6187 (p90) REVERT: B 331 LYS cc_start: 0.9146 (mttt) cc_final: 0.8657 (mttt) REVERT: B 344 TYR cc_start: 0.8424 (t80) cc_final: 0.8037 (t80) REVERT: B 348 TYR cc_start: 0.8127 (t80) cc_final: 0.7778 (t80) REVERT: C 212 LYS cc_start: 0.9322 (mttt) cc_final: 0.9077 (mmmt) REVERT: C 217 GLU cc_start: 0.8391 (mt-10) cc_final: 0.8021 (mt-10) REVERT: C 218 ASP cc_start: 0.8303 (m-30) cc_final: 0.7168 (m-30) REVERT: C 222 ARG cc_start: 0.8955 (mtt-85) cc_final: 0.8386 (mtt-85) REVERT: C 242 VAL cc_start: 0.9055 (t) cc_final: 0.8778 (t) REVERT: C 246 MET cc_start: 0.8904 (mtp) cc_final: 0.8490 (mtp) REVERT: C 249 ASP cc_start: 0.8577 (t70) cc_final: 0.8190 (t70) REVERT: C 257 VAL cc_start: 0.9076 (t) cc_final: 0.8779 (t) REVERT: C 262 MET cc_start: 0.7887 (tmm) cc_final: 0.7075 (tmm) REVERT: C 272 MET cc_start: 0.7832 (mmt) cc_final: 0.7465 (mmt) REVERT: C 275 PHE cc_start: 0.8792 (m-80) cc_final: 0.8291 (m-80) REVERT: C 282 VAL cc_start: 0.8758 (t) cc_final: 0.7831 (t) REVERT: C 302 ASP cc_start: 0.8969 (t0) cc_final: 0.8706 (t0) REVERT: C 316 LYS cc_start: 0.8665 (tppp) cc_final: 0.8102 (tppp) REVERT: C 331 LYS cc_start: 0.9131 (mttm) cc_final: 0.8781 (mttt) REVERT: C 344 TYR cc_start: 0.8500 (t80) cc_final: 0.8083 (t80) REVERT: D 212 LYS cc_start: 0.8943 (mmtm) cc_final: 0.8709 (mmmt) REVERT: D 222 ARG cc_start: 0.8790 (ptp-170) cc_final: 0.8422 (ptp-170) REVERT: D 242 VAL cc_start: 0.8945 (t) cc_final: 0.8640 (t) REVERT: D 245 ASP cc_start: 0.8872 (m-30) cc_final: 0.8562 (m-30) REVERT: D 262 MET cc_start: 0.7761 (tmm) cc_final: 0.7291 (tmm) REVERT: D 267 ASN cc_start: 0.8400 (t0) cc_final: 0.8167 (t0) REVERT: D 275 PHE cc_start: 0.8708 (m-10) cc_final: 0.8408 (m-10) REVERT: D 281 GLU cc_start: 0.7878 (tt0) cc_final: 0.7631 (tt0) REVERT: D 316 LYS cc_start: 0.8527 (mmmm) cc_final: 0.7802 (mmmm) REVERT: D 332 ARG cc_start: 0.8514 (mmt-90) cc_final: 0.8260 (mmt-90) REVERT: D 344 TYR cc_start: 0.8570 (t80) cc_final: 0.8099 (t80) REVERT: D 348 TYR cc_start: 0.8136 (t80) cc_final: 0.7829 (t80) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.1097 time to fit residues: 26.2885 Evaluate side-chains 197 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 36 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 4 optimal weight: 0.0010 chunk 32 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 42 optimal weight: 0.3980 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 ASN B 231 ASN ** B 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.097670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.082449 restraints weight = 12902.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.086154 restraints weight = 6537.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.088652 restraints weight = 3947.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.090396 restraints weight = 2656.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.091677 restraints weight = 1898.310| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.7321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4964 Z= 0.106 Angle : 0.475 5.049 6684 Z= 0.275 Chirality : 0.038 0.125 704 Planarity : 0.003 0.031 888 Dihedral : 3.583 21.772 668 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % 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: 3.39 (0.35), residues: 580 helix: 3.07 (0.24), residues: 408 sheet: None (None), residues: 0 loop : 0.17 (0.53), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 299 TYR 0.010 0.001 TYR A 314 PHE 0.003 0.000 PHE A 284 TRP 0.014 0.001 TRP D 211 Details of bonding type rmsd covalent geometry : bond 0.00203 ( 4964) covalent geometry : angle 0.47532 ( 6684) hydrogen bonds : bond 0.03553 ( 325) hydrogen bonds : angle 3.84121 ( 975) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 TRP cc_start: 0.8182 (m100) cc_final: 0.7270 (m100) REVERT: A 213 LYS cc_start: 0.9125 (mttt) cc_final: 0.8735 (mttt) REVERT: A 221 TRP cc_start: 0.7910 (t-100) cc_final: 0.7573 (t-100) REVERT: A 222 ARG cc_start: 0.8667 (mtt-85) cc_final: 0.8343 (mtt-85) REVERT: A 227 GLU cc_start: 0.8760 (mm-30) cc_final: 0.8039 (mm-30) REVERT: A 262 MET cc_start: 0.8003 (tmm) cc_final: 0.7429 (tmm) REVERT: A 270 MET cc_start: 0.8099 (mtp) cc_final: 0.7803 (mtp) REVERT: A 272 MET cc_start: 0.8248 (mmt) cc_final: 0.7779 (mmt) REVERT: A 275 PHE cc_start: 0.8698 (m-80) cc_final: 0.8319 (m-80) REVERT: A 316 LYS cc_start: 0.8823 (tppp) cc_final: 0.8388 (tppp) REVERT: A 331 LYS cc_start: 0.9227 (mttt) cc_final: 0.8291 (ttmt) REVERT: A 344 TYR cc_start: 0.8113 (t80) cc_final: 0.7710 (t80) REVERT: A 348 TYR cc_start: 0.7697 (t80) cc_final: 0.7466 (t80) REVERT: B 208 MET cc_start: 0.8065 (mmm) cc_final: 0.7676 (mmm) REVERT: B 211 TRP cc_start: 0.8292 (m100) cc_final: 0.7716 (m100) REVERT: B 217 GLU cc_start: 0.7612 (pp20) cc_final: 0.7404 (pp20) REVERT: B 222 ARG cc_start: 0.8760 (mtt-85) cc_final: 0.8321 (mtt-85) REVERT: B 246 MET cc_start: 0.8889 (mtp) cc_final: 0.8514 (mtp) REVERT: B 267 ASN cc_start: 0.7934 (t0) cc_final: 0.7634 (t0) REVERT: B 270 MET cc_start: 0.8104 (mtp) cc_final: 0.7820 (mtp) REVERT: B 272 MET cc_start: 0.7742 (mmt) cc_final: 0.7205 (mmt) REVERT: B 275 PHE cc_start: 0.8639 (m-80) cc_final: 0.8173 (m-80) REVERT: B 316 LYS cc_start: 0.8539 (mmtp) cc_final: 0.7826 (mmtp) REVERT: B 322 TYR cc_start: 0.6748 (p90) cc_final: 0.6254 (p90) REVERT: B 331 LYS cc_start: 0.9148 (mttt) cc_final: 0.8104 (ttmt) REVERT: B 332 ARG cc_start: 0.8748 (tpp-160) cc_final: 0.8481 (mmt-90) REVERT: B 344 TYR cc_start: 0.8453 (t80) cc_final: 0.8048 (t80) REVERT: B 348 TYR cc_start: 0.8121 (t80) cc_final: 0.7764 (t80) REVERT: C 212 LYS cc_start: 0.9327 (mttt) cc_final: 0.9098 (mmmt) REVERT: C 217 GLU cc_start: 0.8331 (mt-10) cc_final: 0.7962 (mt-10) REVERT: C 218 ASP cc_start: 0.8288 (m-30) cc_final: 0.7135 (m-30) REVERT: C 222 ARG cc_start: 0.8916 (mtt-85) cc_final: 0.8356 (mtt-85) REVERT: C 242 VAL cc_start: 0.9054 (t) cc_final: 0.8781 (t) REVERT: C 246 MET cc_start: 0.8836 (mtp) cc_final: 0.8448 (mtp) REVERT: C 249 ASP cc_start: 0.8580 (t70) cc_final: 0.8129 (t70) REVERT: C 257 VAL cc_start: 0.9052 (t) cc_final: 0.8746 (t) REVERT: C 262 MET cc_start: 0.7890 (tmm) cc_final: 0.7057 (tmm) REVERT: C 272 MET cc_start: 0.7903 (mmt) cc_final: 0.7438 (mmt) REVERT: C 275 PHE cc_start: 0.8798 (m-80) cc_final: 0.8319 (m-80) REVERT: C 282 VAL cc_start: 0.8790 (t) cc_final: 0.7874 (t) REVERT: C 316 LYS cc_start: 0.8623 (tppp) cc_final: 0.8052 (tppp) REVERT: C 322 TYR cc_start: 0.6972 (p90) cc_final: 0.6730 (p90) REVERT: C 331 LYS cc_start: 0.9152 (mttm) cc_final: 0.8830 (mttt) REVERT: C 344 TYR cc_start: 0.8487 (t80) cc_final: 0.8059 (t80) REVERT: D 212 LYS cc_start: 0.8965 (mmtm) cc_final: 0.8722 (mmmt) REVERT: D 222 ARG cc_start: 0.8803 (ptp-170) cc_final: 0.8319 (ptp-170) REVERT: D 242 VAL cc_start: 0.8922 (t) cc_final: 0.8609 (t) REVERT: D 245 ASP cc_start: 0.8849 (m-30) cc_final: 0.8540 (m-30) REVERT: D 246 MET cc_start: 0.8452 (ptp) cc_final: 0.8241 (ptp) REVERT: D 262 MET cc_start: 0.7779 (tmm) cc_final: 0.7482 (tmm) REVERT: D 270 MET cc_start: 0.8411 (ttm) cc_final: 0.8030 (tpt) REVERT: D 275 PHE cc_start: 0.8692 (m-10) cc_final: 0.8435 (m-10) REVERT: D 281 GLU cc_start: 0.7910 (tt0) cc_final: 0.7628 (tm-30) REVERT: D 316 LYS cc_start: 0.8495 (mmmm) cc_final: 0.7741 (mmmm) REVERT: D 331 LYS cc_start: 0.9180 (mttm) cc_final: 0.8255 (ttmt) REVERT: D 344 TYR cc_start: 0.8535 (t80) cc_final: 0.8054 (t80) REVERT: D 348 TYR cc_start: 0.8132 (t80) cc_final: 0.7863 (t80) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.1100 time to fit residues: 25.7953 Evaluate side-chains 195 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 30 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 13 optimal weight: 0.0770 chunk 38 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 26 optimal weight: 0.3980 chunk 35 optimal weight: 0.5980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 ASN B 231 ASN ** B 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 ASN ** D 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.096420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.081301 restraints weight = 12919.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.084921 restraints weight = 6625.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.087425 restraints weight = 4057.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.089185 restraints weight = 2723.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.090435 restraints weight = 1945.681| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.7506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4964 Z= 0.115 Angle : 0.499 5.186 6684 Z= 0.288 Chirality : 0.039 0.129 704 Planarity : 0.003 0.036 888 Dihedral : 3.506 14.599 668 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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: 3.33 (0.36), residues: 580 helix: 3.00 (0.24), residues: 408 sheet: None (None), residues: 0 loop : 0.20 (0.54), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 228 TYR 0.010 0.001 TYR A 314 PHE 0.006 0.000 PHE C 350 TRP 0.017 0.002 TRP D 211 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 4964) covalent geometry : angle 0.49863 ( 6684) hydrogen bonds : bond 0.03572 ( 325) hydrogen bonds : angle 3.95869 ( 975) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 TRP cc_start: 0.8173 (m100) cc_final: 0.7278 (m100) REVERT: A 213 LYS cc_start: 0.9137 (mttt) cc_final: 0.8778 (mttt) REVERT: A 221 TRP cc_start: 0.7883 (t-100) cc_final: 0.7623 (t-100) REVERT: A 222 ARG cc_start: 0.8722 (mtt-85) cc_final: 0.8392 (mtt-85) REVERT: A 227 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8072 (mm-30) REVERT: A 247 ARG cc_start: 0.8866 (ttm170) cc_final: 0.8655 (ttm170) REVERT: A 262 MET cc_start: 0.8024 (tmm) cc_final: 0.7485 (tmm) REVERT: A 270 MET cc_start: 0.8088 (mtp) cc_final: 0.7793 (mtp) REVERT: A 272 MET cc_start: 0.8262 (mmt) cc_final: 0.7798 (mmt) REVERT: A 275 PHE cc_start: 0.8673 (m-80) cc_final: 0.8325 (m-80) REVERT: A 299 ARG cc_start: 0.7913 (ttm170) cc_final: 0.7671 (ttm170) REVERT: A 316 LYS cc_start: 0.8780 (tppp) cc_final: 0.8295 (tppp) REVERT: A 344 TYR cc_start: 0.8150 (t80) cc_final: 0.7737 (t80) REVERT: A 348 TYR cc_start: 0.7748 (t80) cc_final: 0.7540 (t80) REVERT: B 208 MET cc_start: 0.8082 (mmm) cc_final: 0.7813 (mmm) REVERT: B 211 TRP cc_start: 0.8276 (m100) cc_final: 0.7605 (m100) REVERT: B 217 GLU cc_start: 0.7615 (pp20) cc_final: 0.7373 (pp20) REVERT: B 222 ARG cc_start: 0.8756 (mtt-85) cc_final: 0.8316 (mtt-85) REVERT: B 246 MET cc_start: 0.8899 (mtp) cc_final: 0.8519 (mtp) REVERT: B 267 ASN cc_start: 0.7982 (t0) cc_final: 0.7627 (t0) REVERT: B 270 MET cc_start: 0.8139 (mtp) cc_final: 0.7849 (mtp) REVERT: B 272 MET cc_start: 0.7744 (mmt) cc_final: 0.7193 (mmt) REVERT: B 275 PHE cc_start: 0.8626 (m-80) cc_final: 0.8183 (m-80) REVERT: B 299 ARG cc_start: 0.7816 (ttm170) cc_final: 0.7520 (ttm170) REVERT: B 316 LYS cc_start: 0.8559 (mmtp) cc_final: 0.7828 (mmtp) REVERT: B 322 TYR cc_start: 0.6799 (p90) cc_final: 0.6294 (p90) REVERT: B 331 LYS cc_start: 0.9146 (mttt) cc_final: 0.8090 (ttmt) REVERT: B 332 ARG cc_start: 0.8742 (tpp-160) cc_final: 0.8540 (mmt-90) REVERT: B 344 TYR cc_start: 0.8457 (t80) cc_final: 0.8041 (t80) REVERT: B 348 TYR cc_start: 0.8096 (t80) cc_final: 0.7730 (t80) REVERT: C 212 LYS cc_start: 0.9335 (mttt) cc_final: 0.9105 (mmmt) REVERT: C 217 GLU cc_start: 0.8381 (mt-10) cc_final: 0.8014 (mt-10) REVERT: C 218 ASP cc_start: 0.8313 (m-30) cc_final: 0.7205 (m-30) REVERT: C 222 ARG cc_start: 0.8902 (mtt-85) cc_final: 0.8450 (mtt-85) REVERT: C 242 VAL cc_start: 0.9069 (t) cc_final: 0.8782 (t) REVERT: C 246 MET cc_start: 0.8835 (mtp) cc_final: 0.8446 (mtp) REVERT: C 249 ASP cc_start: 0.8564 (t70) cc_final: 0.8120 (t70) REVERT: C 257 VAL cc_start: 0.9069 (t) cc_final: 0.8766 (t) REVERT: C 262 MET cc_start: 0.7866 (tmm) cc_final: 0.7033 (tmm) REVERT: C 272 MET cc_start: 0.7910 (mmt) cc_final: 0.7441 (mmt) REVERT: C 275 PHE cc_start: 0.8769 (m-80) cc_final: 0.8304 (m-80) REVERT: C 282 VAL cc_start: 0.8784 (t) cc_final: 0.7877 (t) REVERT: C 316 LYS cc_start: 0.8628 (tppp) cc_final: 0.8052 (tppp) REVERT: C 322 TYR cc_start: 0.7036 (p90) cc_final: 0.6770 (p90) REVERT: C 331 LYS cc_start: 0.9129 (mttm) cc_final: 0.8800 (mttt) REVERT: C 344 TYR cc_start: 0.8480 (t80) cc_final: 0.8068 (t80) REVERT: D 212 LYS cc_start: 0.8978 (mmtm) cc_final: 0.8777 (mmmt) REVERT: D 222 ARG cc_start: 0.8817 (ptp-170) cc_final: 0.8414 (ptp-170) REVERT: D 242 VAL cc_start: 0.8971 (t) cc_final: 0.8669 (t) REVERT: D 245 ASP cc_start: 0.8882 (m-30) cc_final: 0.8561 (m-30) REVERT: D 246 MET cc_start: 0.8438 (ptp) cc_final: 0.8222 (ptp) REVERT: D 262 MET cc_start: 0.7757 (tmm) cc_final: 0.7493 (tmm) REVERT: D 270 MET cc_start: 0.8412 (ttm) cc_final: 0.8036 (tpt) REVERT: D 275 PHE cc_start: 0.8646 (m-10) cc_final: 0.8421 (m-10) REVERT: D 281 GLU cc_start: 0.7890 (tt0) cc_final: 0.7617 (tm-30) REVERT: D 316 LYS cc_start: 0.8527 (mmmm) cc_final: 0.7778 (mmmm) REVERT: D 344 TYR cc_start: 0.8528 (t80) cc_final: 0.8044 (t80) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.1187 time to fit residues: 27.8167 Evaluate side-chains 192 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 0.7980 chunk 26 optimal weight: 0.1980 chunk 15 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 0.4980 chunk 3 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 50 optimal weight: 0.4980 chunk 21 optimal weight: 0.0070 chunk 51 optimal weight: 0.5980 overall best weight: 0.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 ASN B 231 ASN ** B 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 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 = 0.3654 r_free = 0.3654 target = 0.097449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.082166 restraints weight = 12826.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.085846 restraints weight = 6596.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.088370 restraints weight = 4022.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.090106 restraints weight = 2694.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.091396 restraints weight = 1938.470| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.7661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 4964 Z= 0.106 Angle : 0.494 5.240 6684 Z= 0.284 Chirality : 0.039 0.130 704 Planarity : 0.003 0.034 888 Dihedral : 3.478 14.253 668 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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: 3.45 (0.36), residues: 580 helix: 3.12 (0.24), residues: 408 sheet: None (None), residues: 0 loop : 0.18 (0.54), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 228 TYR 0.019 0.001 TYR D 348 PHE 0.004 0.000 PHE C 350 TRP 0.013 0.001 TRP D 211 Details of bonding type rmsd covalent geometry : bond 0.00205 ( 4964) covalent geometry : angle 0.49354 ( 6684) hydrogen bonds : bond 0.03474 ( 325) hydrogen bonds : angle 3.85808 ( 975) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 TRP cc_start: 0.8181 (m100) cc_final: 0.7291 (m100) REVERT: A 213 LYS cc_start: 0.9125 (mttt) cc_final: 0.8765 (mttt) REVERT: A 221 TRP cc_start: 0.7862 (t-100) cc_final: 0.7587 (t-100) REVERT: A 222 ARG cc_start: 0.8689 (mtt-85) cc_final: 0.8343 (mtt-85) REVERT: A 227 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8087 (mm-30) REVERT: A 247 ARG cc_start: 0.8829 (ttm170) cc_final: 0.8621 (ttm170) REVERT: A 262 MET cc_start: 0.7991 (tmm) cc_final: 0.7449 (tmm) REVERT: A 270 MET cc_start: 0.8066 (mtp) cc_final: 0.7794 (mtp) REVERT: A 272 MET cc_start: 0.8240 (mmt) cc_final: 0.7668 (mmt) REVERT: A 275 PHE cc_start: 0.8681 (m-80) cc_final: 0.8385 (m-80) REVERT: A 299 ARG cc_start: 0.7929 (ttm170) cc_final: 0.7669 (ttm170) REVERT: A 316 LYS cc_start: 0.8733 (tppp) cc_final: 0.8227 (tppp) REVERT: A 331 LYS cc_start: 0.9259 (mttt) cc_final: 0.8195 (ttmt) REVERT: A 344 TYR cc_start: 0.8170 (t80) cc_final: 0.7737 (t80) REVERT: A 348 TYR cc_start: 0.7744 (t80) cc_final: 0.7517 (t80) REVERT: B 208 MET cc_start: 0.8061 (mmm) cc_final: 0.7837 (mmm) REVERT: B 211 TRP cc_start: 0.8285 (m100) cc_final: 0.7636 (m100) REVERT: B 222 ARG cc_start: 0.8755 (mtt-85) cc_final: 0.8309 (mtt-85) REVERT: B 246 MET cc_start: 0.8886 (mtp) cc_final: 0.8510 (mtp) REVERT: B 270 MET cc_start: 0.8091 (mtp) cc_final: 0.7799 (mtp) REVERT: B 272 MET cc_start: 0.7693 (mmt) cc_final: 0.7160 (mmt) REVERT: B 275 PHE cc_start: 0.8620 (m-80) cc_final: 0.8196 (m-80) REVERT: B 310 ASN cc_start: 0.9050 (m110) cc_final: 0.8847 (m110) REVERT: B 332 ARG cc_start: 0.8744 (tpp-160) cc_final: 0.8538 (mmt-90) REVERT: B 344 TYR cc_start: 0.8450 (t80) cc_final: 0.8045 (t80) REVERT: C 212 LYS cc_start: 0.9322 (mttt) cc_final: 0.9122 (mmmt) REVERT: C 217 GLU cc_start: 0.8355 (mt-10) cc_final: 0.7980 (mt-10) REVERT: C 218 ASP cc_start: 0.8305 (m-30) cc_final: 0.7232 (m-30) REVERT: C 222 ARG cc_start: 0.8974 (mtt-85) cc_final: 0.8365 (mtt-85) REVERT: C 242 VAL cc_start: 0.9060 (t) cc_final: 0.8769 (t) REVERT: C 246 MET cc_start: 0.8823 (mtp) cc_final: 0.8459 (mtp) REVERT: C 249 ASP cc_start: 0.8557 (t70) cc_final: 0.8111 (t70) REVERT: C 257 VAL cc_start: 0.9065 (t) cc_final: 0.8760 (t) REVERT: C 262 MET cc_start: 0.7848 (tmm) cc_final: 0.7009 (tmm) REVERT: C 275 PHE cc_start: 0.8743 (m-80) cc_final: 0.8338 (m-80) REVERT: C 282 VAL cc_start: 0.8811 (t) cc_final: 0.7924 (t) REVERT: C 316 LYS cc_start: 0.8622 (tppp) cc_final: 0.8023 (tppp) REVERT: C 322 TYR cc_start: 0.7009 (p90) cc_final: 0.6721 (p90) REVERT: C 344 TYR cc_start: 0.8455 (t80) cc_final: 0.8037 (t80) REVERT: D 222 ARG cc_start: 0.8632 (ptp-170) cc_final: 0.8273 (ptp-170) REVERT: D 242 VAL cc_start: 0.8926 (t) cc_final: 0.8634 (t) REVERT: D 245 ASP cc_start: 0.8864 (m-30) cc_final: 0.8562 (m-30) REVERT: D 246 MET cc_start: 0.8430 (ptp) cc_final: 0.8211 (ptp) REVERT: D 262 MET cc_start: 0.7765 (tmm) cc_final: 0.7521 (tmm) REVERT: D 281 GLU cc_start: 0.7931 (tt0) cc_final: 0.7637 (tm-30) REVERT: D 316 LYS cc_start: 0.8388 (mmmm) cc_final: 0.7629 (mmmm) REVERT: D 344 TYR cc_start: 0.8475 (t80) cc_final: 0.7980 (t80) REVERT: D 348 TYR cc_start: 0.7987 (t80) cc_final: 0.7667 (t80) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.1135 time to fit residues: 26.0369 Evaluate side-chains 188 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 52 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 38 optimal weight: 0.2980 chunk 6 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 ASN B 231 ASN C 231 ASN ** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.096403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.081361 restraints weight = 13055.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.084973 restraints weight = 6770.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.087422 restraints weight = 4174.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.089133 restraints weight = 2796.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.090391 restraints weight = 2014.242| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.7863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4964 Z= 0.123 Angle : 0.506 5.229 6684 Z= 0.294 Chirality : 0.039 0.135 704 Planarity : 0.003 0.033 888 Dihedral : 3.595 13.996 668 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: 3.43 (0.36), residues: 580 helix: 3.10 (0.24), residues: 408 sheet: None (None), residues: 0 loop : 0.19 (0.54), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 228 TYR 0.023 0.001 TYR D 348 PHE 0.005 0.001 PHE D 350 TRP 0.021 0.002 TRP D 211 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 4964) covalent geometry : angle 0.50626 ( 6684) hydrogen bonds : bond 0.03537 ( 325) hydrogen bonds : angle 3.93898 ( 975) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1188.17 seconds wall clock time: 21 minutes 15.62 seconds (1275.62 seconds total)