Starting phenix.real_space_refine on Tue Mar 3 12:07:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xor_33357/03_2026/7xor_33357.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xor_33357/03_2026/7xor_33357.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7xor_33357/03_2026/7xor_33357.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xor_33357/03_2026/7xor_33357.map" model { file = "/net/cci-nas-00/data/ceres_data/7xor_33357/03_2026/7xor_33357.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xor_33357/03_2026/7xor_33357.cif" } 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 8 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: 0.97, per 1000 atoms: 0.25 Number of scatterers: 3855 At special positions: 0 Unit cell: (73.08, 87, 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: 0.32 Conformation dependent library (CDL) restraints added in 157.0 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: 19 helices and 7 sheets defined 59.5% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'K' and resid 9 through 29 removed outlier: 4.129A pdb=" N VAL K 29 " --> pdb=" O ASP K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 60 removed outlier: 3.709A 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 Processing helix chain 'K' and resid 201 through 205 removed outlier: 3.590A pdb=" N PHE K 204 " --> pdb=" O SER K 201 " (cutoff:3.500A) Processing helix chain 'K' and resid 233 through 244 removed outlier: 3.529A pdb=" N LEU K 237 " --> pdb=" O MET K 233 " (cutoff:3.500A) Processing helix chain 'K' and resid 256 through 269 Processing helix chain 'K' and resid 282 through 297 removed outlier: 3.541A pdb=" N LYS K 286 " --> pdb=" O GLY K 282 " (cutoff:3.500A) Processing helix chain 'K' and resid 338 through 355 Processing helix chain 'K' and resid 358 through 375 removed outlier: 3.932A 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: 4.075A 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 516 Processing sheet with id=AA1, first strand: chain 'K' and resid 4 through 8 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: 3.541A pdb=" N ALA K 377 " --> pdb=" O VAL K 174 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 193 through 195 Processing sheet with id=AA5, first strand: chain 'K' and resid 273 through 277 removed outlier: 6.289A pdb=" N LEU K 247 " --> pdb=" O ALA K 274 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N VAL K 276 " --> pdb=" O LEU K 247 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ILE K 249 " --> 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 479 268 hydrogen bonds defined for protein. 771 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: 0.59 Time building geometry restraints manager: 0.44 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: 576 1.46 - 1.58: 1930 1.58 - 1.69: 0 1.69 - 1.81: 37 Bond restraints: 3883 Sorted by residual: bond pdb=" CG GLU K 354 " pdb=" CD GLU K 354 " ideal model delta sigma weight residual 1.516 1.488 0.028 2.50e-02 1.60e+03 1.25e+00 bond pdb=" CD GLU K 354 " pdb=" OE1 GLU K 354 " ideal model delta sigma weight residual 1.249 1.230 0.019 1.90e-02 2.77e+03 9.55e-01 bond pdb=" N GLU K 354 " pdb=" CA GLU K 354 " ideal model delta sigma weight residual 1.459 1.470 -0.011 1.19e-02 7.06e+03 8.10e-01 bond pdb=" CA GLU K 355 " pdb=" CB GLU K 355 " ideal model delta sigma weight residual 1.530 1.542 -0.012 1.51e-02 4.39e+03 6.06e-01 bond pdb=" CG1 ILE K 150 " pdb=" CD1 ILE K 150 " ideal model delta sigma weight residual 1.513 1.483 0.030 3.90e-02 6.57e+02 6.06e-01 ... (remaining 3878 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 5038 1.10 - 2.20: 158 2.20 - 3.30: 28 3.30 - 4.40: 15 4.40 - 5.50: 4 Bond angle restraints: 5243 Sorted by residual: angle pdb=" N GLU K 354 " pdb=" CA GLU K 354 " pdb=" CB GLU K 354 " ideal model delta sigma weight residual 110.01 115.51 -5.50 1.45e+00 4.76e-01 1.44e+01 angle pdb=" C GLU K 354 " pdb=" N GLU K 355 " pdb=" CA GLU K 355 " ideal model delta sigma weight residual 122.65 117.51 5.14 1.66e+00 3.63e-01 9.60e+00 angle pdb=" C ILE K 353 " pdb=" N GLU K 354 " pdb=" CA GLU K 354 " ideal model delta sigma weight residual 120.44 116.71 3.73 1.30e+00 5.92e-01 8.21e+00 angle pdb=" N GLY K 486 " pdb=" CA GLY K 486 " pdb=" C GLY K 486 " ideal model delta sigma weight residual 110.46 113.83 -3.37 1.43e+00 4.89e-01 5.57e+00 angle pdb=" N ALA K 449 " pdb=" CA ALA K 449 " pdb=" C ALA K 449 " ideal model delta sigma weight residual 112.75 115.77 -3.02 1.36e+00 5.41e-01 4.94e+00 ... (remaining 5238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 2239 17.98 - 35.97: 142 35.97 - 53.95: 21 53.95 - 71.93: 6 71.93 - 89.92: 4 Dihedral angle restraints: 2412 sinusoidal: 934 harmonic: 1478 Sorted by residual: dihedral pdb=" CB GLU K 102 " pdb=" CG GLU K 102 " pdb=" CD GLU K 102 " pdb=" OE1 GLU K 102 " ideal model delta sinusoidal sigma weight residual 0.00 89.92 -89.92 1 3.00e+01 1.11e-03 1.07e+01 dihedral pdb=" CB MET K 114 " pdb=" CG MET K 114 " pdb=" SD MET K 114 " pdb=" CE MET K 114 " ideal model delta sinusoidal sigma weight residual 60.00 119.85 -59.85 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA GLU K 355 " pdb=" C GLU K 355 " pdb=" N ALA K 356 " pdb=" CA ALA K 356 " ideal model delta harmonic sigma weight residual 180.00 165.55 14.45 0 5.00e+00 4.00e-02 8.35e+00 ... (remaining 2409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 389 0.030 - 0.059: 166 0.059 - 0.089: 53 0.089 - 0.118: 27 0.118 - 0.148: 3 Chirality restraints: 638 Sorted by residual: chirality pdb=" CA GLU K 355 " pdb=" N GLU K 355 " pdb=" C GLU K 355 " pdb=" CB GLU K 355 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" CA GLU K 354 " pdb=" N GLU K 354 " pdb=" C GLU K 354 " pdb=" CB GLU K 354 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.33e-01 chirality pdb=" CA VAL K 136 " pdb=" N VAL K 136 " pdb=" C VAL K 136 " pdb=" CB VAL K 136 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.75e-01 ... (remaining 635 not shown) Planarity restraints: 687 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU K 461 " -0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO K 462 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO K 462 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO K 462 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN K 351 " 0.006 2.00e-02 2.50e+03 1.27e-02 1.62e+00 pdb=" C GLN K 351 " -0.022 2.00e-02 2.50e+03 pdb=" O GLN K 351 " 0.008 2.00e-02 2.50e+03 pdb=" N GLN K 352 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU K 234 " -0.017 5.00e-02 4.00e+02 2.51e-02 1.01e+00 pdb=" N PRO K 235 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO K 235 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO K 235 " -0.014 5.00e-02 4.00e+02 ... (remaining 684 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 937 2.80 - 3.32: 4004 3.32 - 3.85: 6367 3.85 - 4.37: 7060 4.37 - 4.90: 12442 Nonbonded interactions: 30810 Sorted by model distance: nonbonded pdb=" O VAL K 147 " pdb=" OG SER K 151 " model vdw 2.273 3.040 nonbonded pdb=" OD2 ASP K 155 " pdb=" NH2 ARG K 395 " model vdw 2.293 3.120 nonbonded pdb=" OD1 ASP K 291 " pdb=" NH2 ARG K 345 " model vdw 2.306 3.120 nonbonded pdb=" OD1 ASP K 359 " pdb=" NH2 ARG K 362 " model vdw 2.351 3.120 nonbonded pdb=" OD1 ASN K 206 " pdb=" NZ LYS K 272 " model vdw 2.359 3.120 ... (remaining 30805 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: 2.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.320 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 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 0.030 3883 Z= 0.136 Angle : 0.519 5.499 5243 Z= 0.296 Chirality : 0.040 0.148 638 Planarity : 0.003 0.036 687 Dihedral : 12.604 89.918 1464 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % 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: 2.15 (0.36), residues: 522 helix: 2.32 (0.29), residues: 294 sheet: 1.40 (0.61), residues: 72 loop : -0.32 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 268 TYR 0.006 0.001 TYR K 476 PHE 0.008 0.001 PHE K 195 HIS 0.000 0.000 HIS K 401 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 3883) covalent geometry : angle 0.51876 ( 5243) hydrogen bonds : bond 0.14427 ( 268) hydrogen bonds : angle 5.41505 ( 771) *********************** 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 48 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.153 Fit side-chains revert: symmetry clash REVERT: K 105 LYS cc_start: 0.5421 (tmtt) cc_final: 0.5116 (tmtt) REVERT: K 393 LYS cc_start: 0.8749 (tmmt) cc_final: 0.8547 (ttpp) REVERT: K 491 MET cc_start: 0.8914 (mtm) cc_final: 0.8659 (mtp) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.0781 time to fit residues: 4.6537 Evaluate side-chains 31 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.146 ------------------------------------------------------------------------------- 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: 5.9990 chunk 48 optimal weight: 10.0000 chunk 26 optimal weight: 0.0010 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 20.0000 chunk 25 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.078859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.066535 restraints weight = 12056.378| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.86 r_work: 0.3084 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3883 Z= 0.128 Angle : 0.508 6.280 5243 Z= 0.276 Chirality : 0.040 0.136 638 Planarity : 0.003 0.038 687 Dihedral : 3.569 14.140 552 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.50 % Allowed : 8.66 % Favored : 90.84 % 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: 2.22 (0.36), residues: 522 helix: 2.35 (0.28), residues: 301 sheet: 1.16 (0.60), residues: 72 loop : -0.18 (0.50), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 421 TYR 0.008 0.001 TYR K 360 PHE 0.018 0.001 PHE K 195 HIS 0.001 0.000 HIS K 401 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 3883) covalent geometry : angle 0.50845 ( 5243) hydrogen bonds : bond 0.04309 ( 268) hydrogen bonds : angle 4.40342 ( 771) *********************** 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 38 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.140 Fit side-chains revert: symmetry clash REVERT: K 105 LYS cc_start: 0.6221 (tmtt) cc_final: 0.5529 (tttm) REVERT: K 267 MET cc_start: 0.8320 (mmt) cc_final: 0.7798 (mtm) REVERT: K 352 GLN cc_start: 0.8824 (mt0) cc_final: 0.8347 (mt0) REVERT: K 388 GLU cc_start: 0.8366 (mt-10) cc_final: 0.7879 (tp30) outliers start: 2 outliers final: 1 residues processed: 37 average time/residue: 0.0568 time to fit residues: 2.8218 Evaluate side-chains 33 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 236 VAL 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: 10.0000 chunk 48 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 23 optimal weight: 20.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.076547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.063609 restraints weight = 11903.410| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.92 r_work: 0.3021 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3883 Z= 0.193 Angle : 0.513 6.430 5243 Z= 0.278 Chirality : 0.042 0.131 638 Planarity : 0.003 0.027 687 Dihedral : 3.692 15.946 552 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.73 % Allowed : 9.90 % Favored : 88.37 % 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: 2.09 (0.35), residues: 522 helix: 2.29 (0.28), residues: 302 sheet: 1.11 (0.60), residues: 72 loop : -0.39 (0.47), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 322 TYR 0.008 0.001 TYR K 476 PHE 0.015 0.002 PHE K 195 HIS 0.001 0.001 HIS K 401 Details of bonding type rmsd covalent geometry : bond 0.00442 ( 3883) covalent geometry : angle 0.51277 ( 5243) hydrogen bonds : bond 0.04542 ( 268) hydrogen bonds : angle 4.33006 ( 771) *********************** 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 42 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: K 105 LYS cc_start: 0.6266 (tmtt) cc_final: 0.5474 (tttm) REVERT: K 352 GLN cc_start: 0.8823 (mt0) cc_final: 0.8328 (mt0) REVERT: K 366 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7915 (mp10) REVERT: K 388 GLU cc_start: 0.8481 (mt-10) cc_final: 0.7941 (tp30) outliers start: 7 outliers final: 4 residues processed: 40 average time/residue: 0.0672 time to fit residues: 3.4659 Evaluate side-chains 37 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 175 ILE Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 354 GLU Chi-restraints excluded: chain K residue 366 GLN Chi-restraints excluded: chain K residue 385 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 37 optimal weight: 9.9990 chunk 33 optimal weight: 20.0000 chunk 9 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.077801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.064669 restraints weight = 11939.567| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 3.00 r_work: 0.3023 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3883 Z= 0.164 Angle : 0.505 6.384 5243 Z= 0.272 Chirality : 0.041 0.131 638 Planarity : 0.003 0.025 687 Dihedral : 3.719 15.621 552 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.23 % Allowed : 10.40 % Favored : 87.38 % 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: 2.02 (0.36), residues: 522 helix: 2.24 (0.28), residues: 302 sheet: 1.00 (0.60), residues: 72 loop : -0.35 (0.48), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 322 TYR 0.007 0.001 TYR K 476 PHE 0.014 0.001 PHE K 195 HIS 0.000 0.000 HIS K 401 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 3883) covalent geometry : angle 0.50516 ( 5243) hydrogen bonds : bond 0.04274 ( 268) hydrogen bonds : angle 4.29142 ( 771) *********************** 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 42 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.150 Fit side-chains revert: symmetry clash REVERT: K 105 LYS cc_start: 0.6197 (tmtt) cc_final: 0.5361 (tttm) REVERT: K 366 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7910 (mp10) REVERT: K 388 GLU cc_start: 0.8495 (mt-10) cc_final: 0.7955 (tp30) outliers start: 9 outliers final: 5 residues processed: 38 average time/residue: 0.0537 time to fit residues: 2.7150 Evaluate side-chains 37 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 175 ILE Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 354 GLU Chi-restraints excluded: chain K residue 360 TYR Chi-restraints excluded: chain K residue 366 GLN Chi-restraints excluded: chain K residue 385 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: 5.9990 chunk 24 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.077076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.064239 restraints weight = 11945.081| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.97 r_work: 0.3037 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1624 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= 0.142 Angle : 0.476 7.630 5243 Z= 0.257 Chirality : 0.040 0.131 638 Planarity : 0.003 0.027 687 Dihedral : 3.684 15.830 552 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.73 % Allowed : 11.63 % Favored : 86.63 % 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 are not related in a simple way. whole: 2.06 (0.35), residues: 522 helix: 2.29 (0.28), residues: 299 sheet: 0.97 (0.60), residues: 72 loop : -0.32 (0.47), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 322 TYR 0.007 0.001 TYR K 360 PHE 0.013 0.001 PHE K 195 HIS 0.000 0.000 HIS K 401 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 3883) covalent geometry : angle 0.47596 ( 5243) hydrogen bonds : bond 0.04085 ( 268) hydrogen bonds : angle 4.23458 ( 771) *********************** 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 41 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: K 105 LYS cc_start: 0.6255 (tmtt) cc_final: 0.5497 (tttm) REVERT: K 388 GLU cc_start: 0.8482 (mt-10) cc_final: 0.7953 (tp30) outliers start: 7 outliers final: 4 residues processed: 39 average time/residue: 0.0545 time to fit residues: 2.8187 Evaluate side-chains 36 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 175 ILE Chi-restraints excluded: chain K residue 354 GLU Chi-restraints excluded: chain K residue 360 TYR Chi-restraints excluded: chain K residue 385 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 48 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.076319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.063691 restraints weight = 12119.860| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.91 r_work: 0.3028 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1711 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= 0.149 Angle : 0.494 6.272 5243 Z= 0.267 Chirality : 0.041 0.131 638 Planarity : 0.003 0.026 687 Dihedral : 3.678 16.013 552 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.73 % Allowed : 12.13 % Favored : 86.14 % 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: 2.01 (0.35), residues: 522 helix: 2.26 (0.28), residues: 299 sheet: 0.90 (0.59), residues: 72 loop : -0.33 (0.47), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 362 TYR 0.007 0.001 TYR K 360 PHE 0.013 0.001 PHE K 195 HIS 0.000 0.000 HIS K 401 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 3883) covalent geometry : angle 0.49403 ( 5243) hydrogen bonds : bond 0.04122 ( 268) hydrogen bonds : angle 4.22911 ( 771) *********************** 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 40 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.091 Fit side-chains revert: symmetry clash REVERT: K 105 LYS cc_start: 0.6228 (tmtt) cc_final: 0.5456 (tttm) REVERT: K 388 GLU cc_start: 0.8461 (mt-10) cc_final: 0.7943 (tp30) REVERT: K 488 MET cc_start: 0.8828 (mmp) cc_final: 0.8367 (mmt) REVERT: K 518 GLU cc_start: 0.5778 (OUTLIER) cc_final: 0.5260 (mt-10) outliers start: 7 outliers final: 4 residues processed: 38 average time/residue: 0.0558 time to fit residues: 2.7846 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 : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 175 ILE Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 354 GLU Chi-restraints excluded: chain K residue 385 THR Chi-restraints excluded: chain K residue 518 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 4 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 2 optimal weight: 0.0040 chunk 39 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 overall best weight: 2.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.077008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.064385 restraints weight = 12197.960| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.89 r_work: 0.3039 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1752 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= 0.129 Angle : 0.477 6.487 5243 Z= 0.256 Chirality : 0.040 0.133 638 Planarity : 0.003 0.027 687 Dihedral : 3.647 15.917 552 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.24 % Allowed : 13.37 % Favored : 85.40 % 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: 2.12 (0.35), residues: 522 helix: 2.32 (0.28), residues: 300 sheet: 0.96 (0.59), residues: 72 loop : -0.25 (0.48), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 322 TYR 0.007 0.001 TYR K 360 PHE 0.013 0.001 PHE K 195 HIS 0.000 0.000 HIS K 401 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 3883) covalent geometry : angle 0.47687 ( 5243) hydrogen bonds : bond 0.03936 ( 268) hydrogen bonds : angle 4.16094 ( 771) *********************** 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 39 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.147 Fit side-chains revert: symmetry clash REVERT: K 105 LYS cc_start: 0.6208 (tmtt) cc_final: 0.5433 (tttm) REVERT: K 146 GLN cc_start: 0.8583 (tp40) cc_final: 0.8315 (tp40) REVERT: K 267 MET cc_start: 0.8328 (mmt) cc_final: 0.7859 (mtp) REVERT: K 352 GLN cc_start: 0.8574 (mt0) cc_final: 0.8075 (mt0) REVERT: K 388 GLU cc_start: 0.8460 (mt-10) cc_final: 0.7956 (tp30) outliers start: 5 outliers final: 4 residues processed: 37 average time/residue: 0.0489 time to fit residues: 2.4730 Evaluate side-chains 36 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 175 ILE Chi-restraints excluded: chain K residue 354 GLU Chi-restraints excluded: chain K residue 360 TYR Chi-restraints excluded: chain K residue 385 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.075485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.062409 restraints weight = 12168.752| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.97 r_work: 0.2990 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3883 Z= 0.218 Angle : 0.535 6.831 5243 Z= 0.289 Chirality : 0.042 0.142 638 Planarity : 0.003 0.024 687 Dihedral : 3.803 16.378 552 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.98 % Allowed : 12.87 % 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: 1.90 (0.35), residues: 522 helix: 2.13 (0.28), residues: 302 sheet: 0.96 (0.60), residues: 72 loop : -0.39 (0.47), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 322 TYR 0.006 0.001 TYR K 476 PHE 0.011 0.001 PHE K 195 HIS 0.000 0.000 HIS K 401 Details of bonding type rmsd covalent geometry : bond 0.00498 ( 3883) covalent geometry : angle 0.53479 ( 5243) hydrogen bonds : bond 0.04594 ( 268) hydrogen bonds : angle 4.32770 ( 771) *********************** 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 40 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.137 Fit side-chains revert: symmetry clash REVERT: K 105 LYS cc_start: 0.6328 (tmtt) cc_final: 0.5577 (tttm) REVERT: K 146 GLN cc_start: 0.8665 (tp40) cc_final: 0.8389 (tp40) REVERT: K 267 MET cc_start: 0.8356 (mmt) cc_final: 0.7927 (mtp) REVERT: K 352 GLN cc_start: 0.8562 (mt0) cc_final: 0.8136 (mt0) REVERT: K 388 GLU cc_start: 0.8560 (mt-10) cc_final: 0.7987 (tp30) REVERT: K 518 GLU cc_start: 0.5673 (OUTLIER) cc_final: 0.5102 (mt-10) outliers start: 8 outliers final: 5 residues processed: 37 average time/residue: 0.0617 time to fit residues: 3.0017 Evaluate side-chains 38 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 175 ILE Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 354 GLU Chi-restraints excluded: chain K residue 360 TYR Chi-restraints excluded: chain K residue 385 THR Chi-restraints excluded: chain K residue 518 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 0 optimal weight: 8.9990 chunk 19 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 3 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.075953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.062956 restraints weight = 12098.875| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.99 r_work: 0.2997 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3883 Z= 0.181 Angle : 0.509 7.097 5243 Z= 0.275 Chirality : 0.041 0.141 638 Planarity : 0.003 0.025 687 Dihedral : 3.796 15.885 552 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.73 % Allowed : 13.12 % 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: 1.90 (0.35), residues: 522 helix: 2.13 (0.28), residues: 302 sheet: 0.93 (0.60), residues: 72 loop : -0.38 (0.47), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 322 TYR 0.006 0.001 TYR K 476 PHE 0.012 0.001 PHE K 195 HIS 0.000 0.000 HIS K 401 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 3883) covalent geometry : angle 0.50884 ( 5243) hydrogen bonds : bond 0.04365 ( 268) hydrogen bonds : angle 4.25823 ( 771) *********************** 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 40 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.151 Fit side-chains revert: symmetry clash REVERT: K 105 LYS cc_start: 0.6307 (tmtt) cc_final: 0.5539 (tttm) REVERT: K 146 GLN cc_start: 0.8640 (tp40) cc_final: 0.8370 (tp40) REVERT: K 267 MET cc_start: 0.8372 (mmt) cc_final: 0.7932 (mtp) REVERT: K 352 GLN cc_start: 0.8579 (mt0) cc_final: 0.8115 (mt0) REVERT: K 388 GLU cc_start: 0.8535 (mt-10) cc_final: 0.7975 (tp30) REVERT: K 518 GLU cc_start: 0.5652 (OUTLIER) cc_final: 0.5094 (mt-10) outliers start: 7 outliers final: 5 residues processed: 37 average time/residue: 0.0638 time to fit residues: 3.1292 Evaluate side-chains 38 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 175 ILE Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 354 GLU Chi-restraints excluded: chain K residue 360 TYR Chi-restraints excluded: chain K residue 385 THR Chi-restraints excluded: chain K residue 518 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 8 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 42 optimal weight: 8.9990 chunk 12 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.076407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.063419 restraints weight = 12174.514| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.97 r_work: 0.3017 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3883 Z= 0.158 Angle : 0.505 7.206 5243 Z= 0.272 Chirality : 0.041 0.145 638 Planarity : 0.003 0.026 687 Dihedral : 3.758 15.613 552 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.49 % Allowed : 13.12 % Favored : 85.40 % 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: 1.99 (0.35), residues: 522 helix: 2.20 (0.28), residues: 302 sheet: 0.97 (0.60), residues: 72 loop : -0.35 (0.47), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 322 TYR 0.006 0.001 TYR K 360 PHE 0.012 0.001 PHE K 195 HIS 0.000 0.000 HIS K 401 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 3883) covalent geometry : angle 0.50468 ( 5243) hydrogen bonds : bond 0.04191 ( 268) hydrogen bonds : angle 4.19958 ( 771) ********************** 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 40 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.109 Fit side-chains REVERT: K 105 LYS cc_start: 0.6312 (tmtt) cc_final: 0.5532 (tttm) REVERT: K 146 GLN cc_start: 0.8627 (tp40) cc_final: 0.8360 (tp40) REVERT: K 267 MET cc_start: 0.8389 (mmt) cc_final: 0.7942 (mtp) REVERT: K 352 GLN cc_start: 0.8593 (mt0) cc_final: 0.8224 (mt0) REVERT: K 388 GLU cc_start: 0.8519 (mt-10) cc_final: 0.7943 (tp30) REVERT: K 518 GLU cc_start: 0.5614 (OUTLIER) cc_final: 0.5093 (mt-10) outliers start: 6 outliers final: 4 residues processed: 37 average time/residue: 0.0541 time to fit residues: 2.6708 Evaluate side-chains 37 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 175 ILE Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 360 TYR Chi-restraints excluded: chain K residue 385 THR Chi-restraints excluded: chain K residue 518 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 48 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 17 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 25 optimal weight: 20.0000 chunk 26 optimal weight: 0.9980 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.076173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.063185 restraints weight = 12136.634| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.97 r_work: 0.3008 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3883 Z= 0.175 Angle : 0.543 8.280 5243 Z= 0.295 Chirality : 0.042 0.184 638 Planarity : 0.003 0.026 687 Dihedral : 3.769 15.114 552 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.49 % Allowed : 13.37 % 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: 1.88 (0.35), residues: 522 helix: 2.11 (0.28), residues: 302 sheet: 0.95 (0.61), residues: 72 loop : -0.41 (0.47), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 322 TYR 0.006 0.001 TYR K 360 PHE 0.012 0.001 PHE K 195 HIS 0.000 0.000 HIS K 401 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 3883) covalent geometry : angle 0.54290 ( 5243) hydrogen bonds : bond 0.04318 ( 268) hydrogen bonds : angle 4.30554 ( 771) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 784.88 seconds wall clock time: 14 minutes 14.58 seconds (854.58 seconds total)