Starting phenix.real_space_refine on Tue Mar 3 12:07:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xoq_33356/03_2026/7xoq_33356.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xoq_33356/03_2026/7xoq_33356.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xoq_33356/03_2026/7xoq_33356.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xoq_33356/03_2026/7xoq_33356.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xoq_33356/03_2026/7xoq_33356.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xoq_33356/03_2026/7xoq_33356.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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 20 5.16 5 C 2397 2.51 5 N 665 2.21 5 O 773 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3855 Number of models: 1 Model: "" Number of chains: 1 Chain: "K" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Time building chain proxies: 1.04, per 1000 atoms: 0.27 Number of scatterers: 3855 At special positions: 0 Unit cell: (73.08, 84.39, 70.47, 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 20 16.00 O 773 8.00 N 665 7.00 C 2397 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: 0.25 Conformation dependent library (CDL) restraints added in 137.8 milliseconds 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 948 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 7 sheets defined 61.5% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'K' and resid 9 through 28 removed outlier: 3.566A pdb=" N ARG K 13 " --> pdb=" O GLY K 9 " (cutoff:3.500A) Processing helix chain 'K' and resid 29 through 31 No H-bonds generated for 'chain 'K' and resid 29 through 31' Processing helix chain 'K' and resid 52 through 59 removed outlier: 3.932A pdb=" N VAL K 56 " --> pdb=" O ASP K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 64 through 86 Processing helix chain 'K' and resid 88 through 110 Processing helix chain 'K' and resid 112 through 135 Processing helix chain 'K' and resid 140 through 152 Processing helix chain 'K' and resid 155 through 170 removed outlier: 3.569A pdb=" N GLY K 159 " --> pdb=" O ASP K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 201 through 205 removed outlier: 3.521A pdb=" N PHE K 204 " --> pdb=" O SER K 201 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE K 205 " --> pdb=" O PRO K 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 201 through 205' Processing helix chain 'K' and resid 229 through 244 removed outlier: 4.442A pdb=" N MET K 233 " --> pdb=" O ASN K 229 " (cutoff:3.500A) Proline residue: K 235 - end of helix Processing helix chain 'K' and resid 256 through 269 Processing helix chain 'K' and resid 282 through 296 removed outlier: 3.534A pdb=" N LYS K 286 " --> pdb=" O GLY K 282 " (cutoff:3.500A) Processing helix chain 'K' and resid 308 through 312 Processing helix chain 'K' and resid 338 through 355 Processing helix chain 'K' and resid 358 through 375 removed outlier: 4.438A pdb=" N GLY K 375 " --> pdb=" O LYS K 371 " (cutoff:3.500A) Processing helix chain 'K' and resid 385 through 409 Processing helix chain 'K' and resid 416 through 426 Processing helix chain 'K' and resid 433 through 459 Proline residue: K 450 - end of helix Processing helix chain 'K' and resid 461 through 472 removed outlier: 3.550A pdb=" N VAL K 465 " --> pdb=" O GLU K 461 " (cutoff:3.500A) Processing helix chain 'K' and resid 488 through 492 Processing helix chain 'K' and resid 497 through 517 Processing sheet with id=AA1, first strand: chain 'K' and resid 4 through 8 removed outlier: 3.515A pdb=" N THR K 522 " --> pdb=" O ASP K 5 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS K 7 " --> pdb=" O MET K 520 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 38 through 40 Processing sheet with id=AA3, first strand: chain 'K' and resid 174 through 179 removed outlier: 3.858A pdb=" N ASP K 188 " --> pdb=" O VAL K 378 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 192 through 193 removed outlier: 6.667A pdb=" N GLY K 335 " --> pdb=" O ALA K 320 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ALA K 320 " --> pdb=" O GLY K 335 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'K' and resid 192 through 193 removed outlier: 6.667A pdb=" N GLY K 335 " --> pdb=" O ALA K 320 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ALA K 320 " --> pdb=" O GLY K 335 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N PHE K 219 " --> pdb=" O LEU K 248 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ILE K 250 " --> pdb=" O PHE K 219 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU K 221 " --> pdb=" O ILE K 250 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA K 251 " --> pdb=" O VAL K 276 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 411 through 413 Processing sheet with id=AA7, first strand: chain 'K' and resid 476 through 479 267 hydrogen bonds defined for protein. 777 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: 0.67 Time building geometry restraints manager: 0.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1340 1.34 - 1.46: 564 1.46 - 1.58: 1942 1.58 - 1.69: 0 1.69 - 1.81: 37 Bond restraints: 3883 Sorted by residual: bond pdb=" SD MET K 520 " pdb=" CE MET K 520 " ideal model delta sigma weight residual 1.791 1.764 0.027 2.50e-02 1.60e+03 1.17e+00 bond pdb=" CB ASP K 334 " pdb=" CG ASP K 334 " ideal model delta sigma weight residual 1.516 1.539 -0.023 2.50e-02 1.60e+03 8.70e-01 bond pdb=" CB MET K 16 " pdb=" CG MET K 16 " ideal model delta sigma weight residual 1.520 1.494 0.026 3.00e-02 1.11e+03 7.25e-01 bond pdb=" CB MET K 520 " pdb=" CG MET K 520 " ideal model delta sigma weight residual 1.520 1.496 0.024 3.00e-02 1.11e+03 6.21e-01 bond pdb=" N GLY K 477 " pdb=" CA GLY K 477 " ideal model delta sigma weight residual 1.443 1.452 -0.009 1.17e-02 7.31e+03 5.99e-01 ... (remaining 3878 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 5145 1.60 - 3.20: 81 3.20 - 4.81: 12 4.81 - 6.41: 3 6.41 - 8.01: 2 Bond angle restraints: 5243 Sorted by residual: angle pdb=" CB ARG K 197 " pdb=" CG ARG K 197 " pdb=" CD ARG K 197 " ideal model delta sigma weight residual 111.30 118.95 -7.65 2.30e+00 1.89e-01 1.11e+01 angle pdb=" N SER K 139 " pdb=" CA SER K 139 " pdb=" C SER K 139 " ideal model delta sigma weight residual 114.56 110.45 4.11 1.27e+00 6.20e-01 1.05e+01 angle pdb=" N GLU K 354 " pdb=" CA GLU K 354 " pdb=" CB GLU K 354 " ideal model delta sigma weight residual 110.39 115.01 -4.62 1.75e+00 3.27e-01 6.96e+00 angle pdb=" CA LEU K 222 " pdb=" CB LEU K 222 " pdb=" CG LEU K 222 " ideal model delta sigma weight residual 116.30 124.31 -8.01 3.50e+00 8.16e-02 5.24e+00 angle pdb=" C ILE K 353 " pdb=" N GLU K 354 " pdb=" CA GLU K 354 " ideal model delta sigma weight residual 121.18 116.68 4.50 1.98e+00 2.55e-01 5.16e+00 ... (remaining 5238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.45: 2210 15.45 - 30.90: 171 30.90 - 46.35: 25 46.35 - 61.79: 2 61.79 - 77.24: 4 Dihedral angle restraints: 2412 sinusoidal: 934 harmonic: 1478 Sorted by residual: dihedral pdb=" CA ALA K 26 " pdb=" C ALA K 26 " pdb=" N VAL K 27 " pdb=" CA VAL K 27 " ideal model delta harmonic sigma weight residual -180.00 -163.13 -16.87 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA ARG K 197 " pdb=" C ARG K 197 " pdb=" N GLY K 198 " pdb=" CA GLY K 198 " ideal model delta harmonic sigma weight residual 180.00 -163.47 -16.53 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA GLN K 97 " pdb=" CB GLN K 97 " pdb=" CG GLN K 97 " pdb=" CD GLN K 97 " ideal model delta sinusoidal sigma weight residual -60.00 -105.53 45.53 3 1.50e+01 4.44e-03 8.19e+00 ... (remaining 2409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 374 0.025 - 0.051: 150 0.051 - 0.076: 68 0.076 - 0.101: 30 0.101 - 0.127: 16 Chirality restraints: 638 Sorted by residual: chirality pdb=" CA VAL K 213 " pdb=" N VAL K 213 " pdb=" C VAL K 213 " pdb=" CB VAL K 213 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.02e-01 chirality pdb=" CA VAL K 412 " pdb=" N VAL K 412 " pdb=" C VAL K 412 " pdb=" CB VAL K 412 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.65e-01 chirality pdb=" CA ILE K 175 " pdb=" N ILE K 175 " pdb=" C ILE K 175 " pdb=" CB ILE K 175 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.44e-01 ... (remaining 635 not shown) Planarity restraints: 687 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP K 334 " 0.007 2.00e-02 2.50e+03 1.47e-02 2.17e+00 pdb=" C ASP K 334 " -0.025 2.00e-02 2.50e+03 pdb=" O ASP K 334 " 0.010 2.00e-02 2.50e+03 pdb=" N GLY K 335 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG K 197 " -0.090 9.50e-02 1.11e+02 4.06e-02 1.04e+00 pdb=" NE ARG K 197 " 0.004 2.00e-02 2.50e+03 pdb=" CZ ARG K 197 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG K 197 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG K 197 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER K 201 " 0.014 5.00e-02 4.00e+02 2.11e-02 7.13e-01 pdb=" N PRO K 202 " -0.037 5.00e-02 4.00e+02 pdb=" CA PRO K 202 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO K 202 " 0.012 5.00e-02 4.00e+02 ... (remaining 684 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 947 2.80 - 3.33: 4000 3.33 - 3.85: 6383 3.85 - 4.38: 7071 4.38 - 4.90: 12435 Nonbonded interactions: 30836 Sorted by model distance: nonbonded pdb=" O GLU K 339 " pdb=" NE2 GLN K 343 " model vdw 2.277 3.120 nonbonded pdb=" OD2 ASP K 155 " pdb=" NH2 ARG K 395 " model vdw 2.297 3.120 nonbonded pdb=" O ARG K 421 " pdb=" OG SER K 424 " model vdw 2.308 3.040 nonbonded pdb=" NH1 ARG K 421 " pdb=" O GLY K 472 " model vdw 2.339 3.120 nonbonded pdb=" OD1 ASP K 291 " pdb=" NE ARG K 345 " model vdw 2.340 3.120 ... (remaining 30831 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.070 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 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 : 0.003 0.027 3883 Z= 0.143 Angle : 0.543 8.011 5243 Z= 0.305 Chirality : 0.038 0.127 638 Planarity : 0.003 0.041 687 Dihedral : 11.307 77.243 1464 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 are not related in a simple way. whole: 2.13 (0.37), residues: 522 helix: 2.50 (0.30), residues: 293 sheet: 0.35 (0.58), residues: 77 loop : -0.17 (0.52), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 197 TYR 0.012 0.001 TYR K 199 PHE 0.009 0.001 PHE K 195 HIS 0.001 0.001 HIS K 401 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 3883) covalent geometry : angle 0.54306 ( 5243) hydrogen bonds : bond 0.14841 ( 261) hydrogen bonds : angle 5.90458 ( 777) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.151 Fit side-chains REVERT: K 268 ARG cc_start: 0.7603 (mmt-90) cc_final: 0.7162 (mmt180) REVERT: K 433 ASN cc_start: 0.8160 (t0) cc_final: 0.7613 (t0) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0888 time to fit residues: 4.5963 Evaluate side-chains 28 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.4980 chunk 48 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 343 GLN ** K 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 453 GLN K 457 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.075373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.064246 restraints weight = 11438.024| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.97 r_work: 0.3010 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3883 Z= 0.187 Angle : 0.537 6.169 5243 Z= 0.283 Chirality : 0.041 0.141 638 Planarity : 0.003 0.019 687 Dihedral : 3.906 17.020 552 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.99 % Allowed : 5.20 % Favored : 93.81 % 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 are not related in a simple way. whole: 2.20 (0.38), residues: 522 helix: 2.51 (0.30), residues: 298 sheet: 0.27 (0.58), residues: 77 loop : -0.07 (0.54), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 421 TYR 0.009 0.001 TYR K 199 PHE 0.009 0.001 PHE K 195 HIS 0.001 0.001 HIS K 401 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 3883) covalent geometry : angle 0.53715 ( 5243) hydrogen bonds : bond 0.04582 ( 261) hydrogen bonds : angle 4.81817 ( 777) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.125 Fit side-chains REVERT: K 16 MET cc_start: 0.7850 (mtp) cc_final: 0.7512 (mtt) REVERT: K 334 ASP cc_start: 0.8248 (t0) cc_final: 0.7952 (t0) REVERT: K 514 MET cc_start: 0.8702 (mmm) cc_final: 0.8234 (mmm) outliers start: 4 outliers final: 3 residues processed: 34 average time/residue: 0.0643 time to fit residues: 2.9017 Evaluate side-chains 31 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 222 LEU Chi-restraints excluded: chain K residue 311 LYS Chi-restraints excluded: chain K residue 330 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 15 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 48 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 43 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.076099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.064886 restraints weight = 11153.752| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.98 r_work: 0.3025 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3883 Z= 0.136 Angle : 0.495 6.827 5243 Z= 0.258 Chirality : 0.040 0.143 638 Planarity : 0.002 0.019 687 Dihedral : 3.845 16.576 552 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.73 % Allowed : 6.68 % Favored : 91.58 % 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 are not related in a simple way. whole: 2.29 (0.38), residues: 522 helix: 2.65 (0.30), residues: 298 sheet: 0.14 (0.57), residues: 77 loop : -0.06 (0.54), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 421 TYR 0.006 0.001 TYR K 199 PHE 0.009 0.001 PHE K 195 HIS 0.001 0.001 HIS K 401 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 3883) covalent geometry : angle 0.49505 ( 5243) hydrogen bonds : bond 0.04085 ( 261) hydrogen bonds : angle 4.53784 ( 777) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.148 Fit side-chains REVERT: K 334 ASP cc_start: 0.8195 (t0) cc_final: 0.7841 (t0) REVERT: K 514 MET cc_start: 0.8562 (mmm) cc_final: 0.8316 (mmm) outliers start: 7 outliers final: 3 residues processed: 35 average time/residue: 0.0642 time to fit residues: 3.0016 Evaluate side-chains 30 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 27 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 222 LEU Chi-restraints excluded: chain K residue 311 LYS Chi-restraints excluded: chain K residue 330 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 37 optimal weight: 0.0970 chunk 33 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 19 optimal weight: 10.0000 chunk 42 optimal weight: 0.8980 chunk 18 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 chunk 14 optimal weight: 9.9990 chunk 20 optimal weight: 0.5980 chunk 17 optimal weight: 5.9990 overall best weight: 1.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.076426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.065547 restraints weight = 11133.082| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.90 r_work: 0.3045 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3883 Z= 0.117 Angle : 0.481 7.376 5243 Z= 0.249 Chirality : 0.040 0.141 638 Planarity : 0.002 0.019 687 Dihedral : 3.771 16.234 552 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.99 % Allowed : 9.16 % Favored : 89.85 % 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 are not related in a simple way. whole: 2.36 (0.38), residues: 522 helix: 2.75 (0.30), residues: 298 sheet: 0.04 (0.57), residues: 77 loop : -0.07 (0.54), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 421 TYR 0.006 0.001 TYR K 478 PHE 0.009 0.001 PHE K 195 HIS 0.001 0.001 HIS K 401 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 3883) covalent geometry : angle 0.48102 ( 5243) hydrogen bonds : bond 0.03850 ( 261) hydrogen bonds : angle 4.38479 ( 777) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.129 Fit side-chains REVERT: K 114 MET cc_start: 0.8724 (mmm) cc_final: 0.8520 (mmm) REVERT: K 311 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8083 (mptt) REVERT: K 334 ASP cc_start: 0.8168 (t0) cc_final: 0.7842 (t0) outliers start: 4 outliers final: 2 residues processed: 34 average time/residue: 0.0638 time to fit residues: 2.8775 Evaluate side-chains 31 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 222 LEU Chi-restraints excluded: chain K residue 311 LYS Chi-restraints excluded: chain K residue 330 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 24 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 31 optimal weight: 8.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.075840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.064655 restraints weight = 11272.348| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.98 r_work: 0.3022 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3883 Z= 0.138 Angle : 0.485 7.428 5243 Z= 0.253 Chirality : 0.040 0.136 638 Planarity : 0.002 0.018 687 Dihedral : 3.739 16.299 552 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.73 % Allowed : 11.88 % Favored : 86.39 % 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 are not related in a simple way. whole: 2.36 (0.38), residues: 522 helix: 2.82 (0.30), residues: 297 sheet: -0.07 (0.58), residues: 72 loop : -0.15 (0.53), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 58 TYR 0.006 0.001 TYR K 478 PHE 0.006 0.001 PHE K 8 HIS 0.001 0.001 HIS K 401 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 3883) covalent geometry : angle 0.48525 ( 5243) hydrogen bonds : bond 0.03984 ( 261) hydrogen bonds : angle 4.32709 ( 777) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: K 334 ASP cc_start: 0.8152 (t0) cc_final: 0.7819 (t0) outliers start: 7 outliers final: 5 residues processed: 37 average time/residue: 0.0638 time to fit residues: 3.1584 Evaluate side-chains 36 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 222 LEU Chi-restraints excluded: chain K residue 270 ILE Chi-restraints excluded: chain K residue 311 LYS Chi-restraints excluded: chain K residue 330 THR Chi-restraints excluded: chain K residue 354 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 13 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 chunk 36 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.073693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.062473 restraints weight = 11689.049| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.98 r_work: 0.2962 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 3883 Z= 0.242 Angle : 0.562 6.790 5243 Z= 0.296 Chirality : 0.043 0.140 638 Planarity : 0.003 0.024 687 Dihedral : 3.997 17.412 552 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.24 % Allowed : 13.61 % Favored : 85.15 % 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 are not related in a simple way. whole: 2.10 (0.37), residues: 522 helix: 2.56 (0.30), residues: 294 sheet: -0.21 (0.58), residues: 72 loop : -0.07 (0.52), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 58 TYR 0.007 0.001 TYR K 199 PHE 0.009 0.002 PHE K 195 HIS 0.001 0.001 HIS K 401 Details of bonding type rmsd covalent geometry : bond 0.00551 ( 3883) covalent geometry : angle 0.56166 ( 5243) hydrogen bonds : bond 0.04692 ( 261) hydrogen bonds : angle 4.56581 ( 777) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.158 Fit side-chains revert: symmetry clash REVERT: K 114 MET cc_start: 0.8883 (mmm) cc_final: 0.8644 (mmt) REVERT: K 334 ASP cc_start: 0.8228 (t0) cc_final: 0.7873 (t0) REVERT: K 514 MET cc_start: 0.8611 (mmm) cc_final: 0.8405 (mmm) outliers start: 5 outliers final: 5 residues processed: 34 average time/residue: 0.0662 time to fit residues: 3.0106 Evaluate side-chains 32 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 222 LEU Chi-restraints excluded: chain K residue 270 ILE Chi-restraints excluded: chain K residue 311 LYS Chi-restraints excluded: chain K residue 330 THR Chi-restraints excluded: chain K residue 354 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 4 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 0.3980 chunk 2 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 15 optimal weight: 10.0000 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.076481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.065241 restraints weight = 11509.283| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 3.03 r_work: 0.3033 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3883 Z= 0.107 Angle : 0.470 7.627 5243 Z= 0.246 Chirality : 0.040 0.138 638 Planarity : 0.002 0.018 687 Dihedral : 3.751 15.636 552 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.73 % Allowed : 13.61 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.40 (0.38), residues: 522 helix: 2.89 (0.30), residues: 297 sheet: -0.23 (0.60), residues: 72 loop : -0.12 (0.53), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 421 TYR 0.007 0.001 TYR K 476 PHE 0.010 0.001 PHE K 195 HIS 0.001 0.000 HIS K 401 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 3883) covalent geometry : angle 0.46999 ( 5243) hydrogen bonds : bond 0.03848 ( 261) hydrogen bonds : angle 4.23730 ( 777) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.090 Fit side-chains revert: symmetry clash REVERT: K 334 ASP cc_start: 0.8211 (t0) cc_final: 0.7854 (t0) REVERT: K 520 MET cc_start: 0.8754 (mmm) cc_final: 0.8474 (mtt) outliers start: 7 outliers final: 5 residues processed: 35 average time/residue: 0.0632 time to fit residues: 2.9263 Evaluate side-chains 34 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 222 LEU Chi-restraints excluded: chain K residue 270 ILE Chi-restraints excluded: chain K residue 311 LYS Chi-restraints excluded: chain K residue 330 THR Chi-restraints excluded: chain K residue 354 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 32 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 44 optimal weight: 0.9980 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.074726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.063534 restraints weight = 11488.221| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.98 r_work: 0.2993 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3883 Z= 0.184 Angle : 0.522 6.942 5243 Z= 0.271 Chirality : 0.041 0.136 638 Planarity : 0.003 0.018 687 Dihedral : 3.825 16.358 552 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.98 % Allowed : 13.37 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.38), residues: 522 helix: 2.77 (0.30), residues: 296 sheet: -0.30 (0.59), residues: 72 loop : -0.06 (0.52), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 430 TYR 0.006 0.001 TYR K 478 PHE 0.008 0.001 PHE K 195 HIS 0.001 0.001 HIS K 401 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 3883) covalent geometry : angle 0.52167 ( 5243) hydrogen bonds : bond 0.04242 ( 261) hydrogen bonds : angle 4.35623 ( 777) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.156 Fit side-chains revert: symmetry clash REVERT: K 334 ASP cc_start: 0.8204 (t0) cc_final: 0.7842 (t0) REVERT: K 520 MET cc_start: 0.8850 (mmm) cc_final: 0.8502 (mtt) outliers start: 8 outliers final: 4 residues processed: 37 average time/residue: 0.0612 time to fit residues: 3.0560 Evaluate side-chains 32 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 222 LEU Chi-restraints excluded: chain K residue 270 ILE Chi-restraints excluded: chain K residue 330 THR Chi-restraints excluded: chain K residue 354 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.075555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.064339 restraints weight = 11397.480| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.99 r_work: 0.3014 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3883 Z= 0.138 Angle : 0.506 7.617 5243 Z= 0.261 Chirality : 0.040 0.135 638 Planarity : 0.002 0.017 687 Dihedral : 3.775 15.645 552 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.99 % Allowed : 14.11 % Favored : 84.90 % 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 are not related in a simple way. whole: 2.33 (0.38), residues: 522 helix: 2.85 (0.30), residues: 296 sheet: -0.32 (0.59), residues: 72 loop : -0.11 (0.52), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 421 TYR 0.006 0.001 TYR K 478 PHE 0.009 0.001 PHE K 195 HIS 0.001 0.001 HIS K 401 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 3883) covalent geometry : angle 0.50573 ( 5243) hydrogen bonds : bond 0.04035 ( 261) hydrogen bonds : angle 4.28053 ( 777) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.204 Fit side-chains revert: symmetry clash REVERT: K 334 ASP cc_start: 0.8165 (t0) cc_final: 0.7808 (t0) outliers start: 4 outliers final: 4 residues processed: 34 average time/residue: 0.0616 time to fit residues: 2.8376 Evaluate side-chains 33 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 222 LEU Chi-restraints excluded: chain K residue 270 ILE Chi-restraints excluded: chain K residue 330 THR Chi-restraints excluded: chain K residue 354 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 8 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 45 optimal weight: 0.0370 chunk 39 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 42 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.5864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.076405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.065444 restraints weight = 11480.702| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.96 r_work: 0.3046 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3883 Z= 0.115 Angle : 0.507 7.871 5243 Z= 0.262 Chirality : 0.040 0.136 638 Planarity : 0.002 0.018 687 Dihedral : 3.729 15.757 552 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.99 % Allowed : 14.36 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.37 (0.38), residues: 522 helix: 2.89 (0.30), residues: 297 sheet: -0.27 (0.60), residues: 72 loop : -0.15 (0.52), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 421 TYR 0.007 0.001 TYR K 476 PHE 0.009 0.001 PHE K 195 HIS 0.001 0.001 HIS K 401 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 3883) covalent geometry : angle 0.50730 ( 5243) hydrogen bonds : bond 0.03885 ( 261) hydrogen bonds : angle 4.22681 ( 777) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.140 Fit side-chains revert: symmetry clash REVERT: K 311 LYS cc_start: 0.8693 (ptpp) cc_final: 0.7873 (mtpp) REVERT: K 334 ASP cc_start: 0.8113 (t0) cc_final: 0.7769 (t0) outliers start: 4 outliers final: 4 residues processed: 34 average time/residue: 0.0644 time to fit residues: 2.9530 Evaluate side-chains 33 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 222 LEU Chi-restraints excluded: chain K residue 270 ILE Chi-restraints excluded: chain K residue 330 THR Chi-restraints excluded: chain K residue 354 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 48 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.075668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.064851 restraints weight = 11451.256| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.91 r_work: 0.3032 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3883 Z= 0.145 Angle : 0.534 8.845 5243 Z= 0.274 Chirality : 0.041 0.168 638 Planarity : 0.002 0.018 687 Dihedral : 3.772 15.844 552 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.24 % Allowed : 14.11 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.38), residues: 522 helix: 2.72 (0.30), residues: 297 sheet: -0.33 (0.59), residues: 72 loop : -0.14 (0.51), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 421 TYR 0.006 0.001 TYR K 478 PHE 0.008 0.001 PHE K 195 HIS 0.001 0.001 HIS K 401 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 3883) covalent geometry : angle 0.53441 ( 5243) hydrogen bonds : bond 0.04066 ( 261) hydrogen bonds : angle 4.26566 ( 777) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 865.28 seconds wall clock time: 15 minutes 32.84 seconds (932.84 seconds total)