Starting phenix.real_space_refine on Tue Aug 4 19:36:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9czc_46410/08_2026/9czc_46410.cif Found real_map, /net/cci-nas-00/data/ceres_data/9czc_46410/08_2026/9czc_46410.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9czc_46410/08_2026/9czc_46410.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9czc_46410/08_2026/9czc_46410.map" model { file = "/net/cci-nas-00/data/ceres_data/9czc_46410/08_2026/9czc_46410.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9czc_46410/08_2026/9czc_46410.cif" } resolution = 3.7 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= 0.024 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 14 5.16 5 C 3971 2.51 5 N 1030 2.21 5 O 1199 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6214 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 6214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 796, 6214 Classifications: {'peptide': 796} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 29, 'TRANS': 766} Chain breaks: 2 Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 221 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 7, 'ASN:plan1': 8, 'ASP:plan': 8, 'ARG:plan': 1, 'TYR:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 112 Time building chain proxies: 1.32, per 1000 atoms: 0.21 Number of scatterers: 6214 At special positions: 0 Unit cell: (67.768, 99.288, 112.684, 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 14 16.00 O 1199 8.00 N 1030 7.00 C 3971 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 412 " - pdb=" SG CYS B 426 " distance=2.03 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: 0.38 Conformation dependent library (CDL) restraints added in 353.8 milliseconds 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1518 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 10 sheets defined 49.5% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'B' and resid 51 through 56 Processing helix chain 'B' and resid 76 through 96 Processing helix chain 'B' and resid 97 through 109 Processing helix chain 'B' and resid 205 through 222 removed outlier: 3.519A pdb=" N THR B 209 " --> pdb=" O ASP B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 256 Processing helix chain 'B' and resid 257 through 263 Processing helix chain 'B' and resid 264 through 288 removed outlier: 3.701A pdb=" N LYS B 288 " --> pdb=" O SER B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 295 No H-bonds generated for 'chain 'B' and resid 293 through 295' Processing helix chain 'B' and resid 296 through 307 removed outlier: 4.179A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ASP B 301 " --> pdb=" O ASN B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 334 removed outlier: 3.651A pdb=" N ASN B 325 " --> pdb=" O ILE B 321 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP B 326 " --> pdb=" O ASN B 322 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE B 327 " --> pdb=" O LYS B 323 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N PHE B 334 " --> pdb=" O LYS B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 344 Processing helix chain 'B' and resid 377 through 388 removed outlier: 5.104A pdb=" N ASN B 383 " --> pdb=" O LEU B 380 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N GLY B 386 " --> pdb=" O ASN B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 394 No H-bonds generated for 'chain 'B' and resid 392 through 394' Processing helix chain 'B' and resid 432 through 434 No H-bonds generated for 'chain 'B' and resid 432 through 434' Processing helix chain 'B' and resid 444 through 450 removed outlier: 4.131A pdb=" N ASN B 447 " --> pdb=" O ASN B 444 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR B 450 " --> pdb=" O ASN B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 525 Processing helix chain 'B' and resid 540 through 547 removed outlier: 3.699A pdb=" N ALA B 544 " --> pdb=" O SER B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 565 Processing helix chain 'B' and resid 568 through 570 No H-bonds generated for 'chain 'B' and resid 568 through 570' Processing helix chain 'B' and resid 571 through 588 removed outlier: 4.212A pdb=" N THR B 584 " --> pdb=" O LEU B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 610 Processing helix chain 'B' and resid 614 through 620 Processing helix chain 'B' and resid 620 through 629 Processing helix chain 'B' and resid 630 through 634 Processing helix chain 'B' and resid 660 through 693 removed outlier: 4.018A pdb=" N ILE B 664 " --> pdb=" O LYS B 660 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS B 665 " --> pdb=" O ASN B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 725 Processing helix chain 'B' and resid 727 through 734 Processing helix chain 'B' and resid 739 through 800 removed outlier: 3.513A pdb=" N ASN B 757 " --> pdb=" O ILE B 753 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LEU B 782 " --> pdb=" O LYS B 778 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ARG B 783 " --> pdb=" O ILE B 779 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU B 784 " --> pdb=" O ASN B 780 " (cutoff:3.500A) Processing helix chain 'B' and resid 800 through 805 Processing helix chain 'B' and resid 807 through 819 Processing sheet with id=AA1, first strand: chain 'B' and resid 161 through 164 removed outlier: 6.427A pdb=" N TRP B 40 " --> pdb=" O ILE B 150 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE B 41 " --> pdb=" O ASN B 34 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N ASN B 34 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU B 133 " --> pdb=" O LYS B 22 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU B 486 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 60 through 61 Processing sheet with id=AA3, first strand: chain 'B' and resid 66 through 67 Processing sheet with id=AA4, first strand: chain 'B' and resid 166 through 167 removed outlier: 4.113A pdb=" N SER B 166 " --> pdb=" O TYR B 497 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 201 through 203 removed outlier: 4.187A pdb=" N LYS B 356 " --> pdb=" O ARG B 193 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 232 through 233 removed outlier: 3.581A pdb=" N THR B 247 " --> pdb=" O ILE B 233 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 309 through 311 Processing sheet with id=AA8, first strand: chain 'B' and resid 422 through 430 removed outlier: 4.243A pdb=" N GLU B 510 " --> pdb=" O ILE B 408 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 536 through 538 removed outlier: 6.384A pdb=" N ASN B 536 " --> pdb=" O ILE B 551 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 591 through 592 314 hydrogen bonds defined for protein. 867 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: 0.72 Time building geometry restraints manager: 0.52 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: 2033 1.34 - 1.46: 1413 1.46 - 1.58: 2860 1.58 - 1.70: 0 1.70 - 1.82: 24 Bond restraints: 6330 Sorted by residual: bond pdb=" CB TYR B 443 " pdb=" CG TYR B 443 " ideal model delta sigma weight residual 1.512 1.478 0.034 2.20e-02 2.07e+03 2.38e+00 bond pdb=" CA TYR B 443 " pdb=" CB TYR B 443 " ideal model delta sigma weight residual 1.532 1.504 0.027 1.82e-02 3.02e+03 2.27e+00 bond pdb=" CG ASN B 325 " pdb=" ND2 ASN B 325 " ideal model delta sigma weight residual 1.328 1.297 0.031 2.10e-02 2.27e+03 2.19e+00 bond pdb=" CZ TYR B 443 " pdb=" OH TYR B 443 " ideal model delta sigma weight residual 1.376 1.346 0.030 2.10e-02 2.27e+03 2.05e+00 bond pdb=" CB ASN B 325 " pdb=" CG ASN B 325 " ideal model delta sigma weight residual 1.516 1.482 0.034 2.50e-02 1.60e+03 1.81e+00 ... (remaining 6325 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 8360 1.33 - 2.66: 183 2.66 - 4.00: 34 4.00 - 5.33: 9 5.33 - 6.66: 6 Bond angle restraints: 8592 Sorted by residual: angle pdb=" CA GLU B 635 " pdb=" CB GLU B 635 " pdb=" CG GLU B 635 " ideal model delta sigma weight residual 114.10 120.76 -6.66 2.00e+00 2.50e-01 1.11e+01 angle pdb=" C ASN B 325 " pdb=" CA ASN B 325 " pdb=" CB ASN B 325 " ideal model delta sigma weight residual 110.79 105.77 5.02 1.66e+00 3.63e-01 9.14e+00 angle pdb=" CA LYS B 679 " pdb=" CB LYS B 679 " pdb=" CG LYS B 679 " ideal model delta sigma weight residual 114.10 120.11 -6.01 2.00e+00 2.50e-01 9.03e+00 angle pdb=" CG ARG B 394 " pdb=" CD ARG B 394 " pdb=" NE ARG B 394 " ideal model delta sigma weight residual 112.00 117.70 -5.70 2.20e+00 2.07e-01 6.70e+00 angle pdb=" CA ILE B 263 " pdb=" CB ILE B 263 " pdb=" CG1 ILE B 263 " ideal model delta sigma weight residual 110.40 114.77 -4.37 1.70e+00 3.46e-01 6.62e+00 ... (remaining 8587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 3276 17.94 - 35.87: 389 35.87 - 53.81: 121 53.81 - 71.74: 29 71.74 - 89.68: 14 Dihedral angle restraints: 3829 sinusoidal: 1482 harmonic: 2347 Sorted by residual: dihedral pdb=" CA SER B 822 " pdb=" C SER B 822 " pdb=" N ILE B 823 " pdb=" CA ILE B 823 " ideal model delta harmonic sigma weight residual -180.00 -158.33 -21.67 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA ILE B 823 " pdb=" C ILE B 823 " pdb=" N PRO B 824 " pdb=" CA PRO B 824 " ideal model delta harmonic sigma weight residual 180.00 159.36 20.64 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA ASN B 821 " pdb=" C ASN B 821 " pdb=" N SER B 822 " pdb=" CA SER B 822 " ideal model delta harmonic sigma weight residual 180.00 -159.64 -20.36 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 3826 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 566 0.030 - 0.059: 274 0.059 - 0.088: 82 0.088 - 0.118: 50 0.118 - 0.147: 14 Chirality restraints: 986 Sorted by residual: chirality pdb=" CB THR B 791 " pdb=" CA THR B 791 " pdb=" OG1 THR B 791 " pdb=" CG2 THR B 791 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.43e-01 chirality pdb=" CA ILE B 149 " pdb=" N ILE B 149 " pdb=" C ILE B 149 " pdb=" CB ILE B 149 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.58e-01 chirality pdb=" CA ILE B 183 " pdb=" N ILE B 183 " pdb=" C ILE B 183 " pdb=" CB ILE B 183 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.28e-01 ... (remaining 983 not shown) Planarity restraints: 1116 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 823 " 0.049 5.00e-02 4.00e+02 7.46e-02 8.89e+00 pdb=" N PRO B 824 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO B 824 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 824 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 154 " -0.032 5.00e-02 4.00e+02 4.89e-02 3.83e+00 pdb=" N PRO B 155 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 155 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 155 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 436 " 0.009 2.00e-02 2.50e+03 1.04e-02 1.91e+00 pdb=" CG PHE B 436 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE B 436 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE B 436 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE B 436 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 436 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 436 " 0.001 2.00e-02 2.50e+03 ... (remaining 1113 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 600 2.74 - 3.28: 6333 3.28 - 3.82: 10729 3.82 - 4.36: 12564 4.36 - 4.90: 21777 Nonbonded interactions: 52003 Sorted by model distance: nonbonded pdb=" O LEU B 157 " pdb=" OG SER B 187 " model vdw 2.203 3.040 nonbonded pdb=" O VAL B 567 " pdb=" OH TYR B 726 " model vdw 2.209 3.040 nonbonded pdb=" OH TYR B 443 " pdb=" OG SER B 687 " model vdw 2.230 3.040 nonbonded pdb=" O SER B 108 " pdb=" ND2 ASN B 147 " model vdw 2.241 3.120 nonbonded pdb=" O TYR B 522 " pdb=" NE2 GLN B 526 " model vdw 2.258 3.120 ... (remaining 51998 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.610 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.040 Find NCS groups from input model: 0.030 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 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 : 0.004 0.037 6331 Z= 0.174 Angle : 0.538 6.660 8594 Z= 0.292 Chirality : 0.043 0.147 986 Planarity : 0.004 0.075 1116 Dihedral : 18.238 89.677 2308 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 5.04 % Allowed : 26.41 % Favored : 68.55 % 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: 0.33 (0.30), residues: 790 helix: 1.25 (0.28), residues: 351 sheet: -0.15 (0.59), residues: 85 loop : -0.68 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 394 TYR 0.012 0.001 TYR B 443 PHE 0.024 0.002 PHE B 436 TRP 0.010 0.002 TRP B 40 HIS 0.002 0.000 HIS B 512 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.17 ( 6330) covalent geometry : angle 0.53754 / 0.29 ( 8592) SS BOND : bond 0.00050 / 0.03 ( 1) SS BOND : angle 1.92549 / 1.03 ( 2) hydrogen bonds : bond 0.12568 / 8.32 ( 314) hydrogen bonds : angle 5.52184 / 3.72 ( 867) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 62 time to evaluate : 0.235 Fit side-chains REVERT: B 316 ILE cc_start: 0.6556 (mm) cc_final: 0.6318 (mm) outliers start: 34 outliers final: 31 residues processed: 95 average time/residue: 0.0539 time to fit residues: 7.2357 Evaluate side-chains 91 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 60 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 274 ASN Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 379 ASN Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 442 SER Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 647 VAL Chi-restraints excluded: chain B residue 731 LYS Chi-restraints excluded: chain B residue 752 SER Chi-restraints excluded: chain B residue 768 SER Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 818 THR Chi-restraints excluded: chain B residue 819 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 0.0770 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.0170 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.0570 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 0.5980 overall best weight: 0.2694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 274 ASN B 325 ASN ** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.165030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.137343 restraints weight = 65275.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.142343 restraints weight = 44725.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.140115 restraints weight = 30993.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.140410 restraints weight = 31623.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.140362 restraints weight = 29643.822| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6331 Z= 0.097 Angle : 0.443 4.585 8594 Z= 0.241 Chirality : 0.041 0.133 986 Planarity : 0.004 0.054 1116 Dihedral : 7.308 58.072 893 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.15 % Allowed : 24.18 % Favored : 71.66 % 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: 1.02 (0.31), residues: 790 helix: 1.92 (0.28), residues: 352 sheet: 0.02 (0.62), residues: 77 loop : -0.38 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 394 TYR 0.008 0.001 TYR B 307 PHE 0.013 0.001 PHE B 436 TRP 0.007 0.001 TRP B 40 HIS 0.001 0.000 HIS B 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 ( 6330) covalent geometry : angle 0.44214 / 0.24 ( 8592) SS BOND : bond 0.00141 / 0.07 ( 1) SS BOND : angle 2.07228 / 1.11 ( 2) hydrogen bonds : bond 0.03720 / 2.44 ( 314) hydrogen bonds : angle 4.01551 / 2.70 ( 867) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 76 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: B 316 ILE cc_start: 0.7048 (mm) cc_final: 0.6847 (mm) REVERT: B 330 LYS cc_start: 0.7685 (OUTLIER) cc_final: 0.7073 (tptp) REVERT: B 427 ILE cc_start: 0.7128 (OUTLIER) cc_final: 0.6460 (pp) REVERT: B 578 GLN cc_start: 0.8357 (mm-40) cc_final: 0.8028 (tp-100) REVERT: B 679 LYS cc_start: 0.5663 (mmpt) cc_final: 0.4516 (ttpt) outliers start: 28 outliers final: 13 residues processed: 100 average time/residue: 0.0581 time to fit residues: 8.0020 Evaluate side-chains 83 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 274 ASN Chi-restraints excluded: chain B residue 330 LYS Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 518 ASN Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 814 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 27 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 17 optimal weight: 0.0270 chunk 36 optimal weight: 3.9990 chunk 12 optimal weight: 0.0970 chunk 32 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 39 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 52.1468 > 50:) chunk 9 optimal weight: 0.9980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 235 GLN ** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.163765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.135963 restraints weight = 65676.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.139073 restraints weight = 44634.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.138520 restraints weight = 33590.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.138798 restraints weight = 32832.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.138719 restraints weight = 31185.163| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6331 Z= 0.110 Angle : 0.443 7.002 8594 Z= 0.237 Chirality : 0.041 0.142 986 Planarity : 0.004 0.049 1116 Dihedral : 5.625 58.956 860 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.71 % Allowed : 24.48 % Favored : 71.81 % 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: 1.05 (0.31), residues: 790 helix: 1.96 (0.28), residues: 352 sheet: -0.03 (0.59), residues: 85 loop : -0.37 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 410 TYR 0.009 0.001 TYR B 796 PHE 0.011 0.001 PHE B 761 TRP 0.003 0.001 TRP B 40 HIS 0.001 0.000 HIS B 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 6330) covalent geometry : angle 0.44145 / 0.24 ( 8592) SS BOND : bond 0.00135 / 0.07 ( 1) SS BOND : angle 2.11824 / 1.13 ( 2) hydrogen bonds : bond 0.03608 / 2.32 ( 314) hydrogen bonds : angle 3.84383 / 2.58 ( 867) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: B 78 GLU cc_start: 0.6674 (mm-30) cc_final: 0.6361 (tp30) REVERT: B 316 ILE cc_start: 0.7000 (mm) cc_final: 0.6798 (mm) REVERT: B 330 LYS cc_start: 0.7705 (OUTLIER) cc_final: 0.6998 (tptp) REVERT: B 427 ILE cc_start: 0.7075 (OUTLIER) cc_final: 0.6411 (pp) REVERT: B 577 GLN cc_start: 0.5990 (tp40) cc_final: 0.5265 (tt0) REVERT: B 578 GLN cc_start: 0.8430 (mm-40) cc_final: 0.8184 (tp-100) REVERT: B 679 LYS cc_start: 0.5889 (mmpt) cc_final: 0.5298 (mmpt) outliers start: 25 outliers final: 13 residues processed: 96 average time/residue: 0.0565 time to fit residues: 7.3933 Evaluate side-chains 86 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 330 LYS Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 375 TYR Chi-restraints excluded: chain B residue 379 ASN Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 814 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 42 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 45 optimal weight: 0.3980 chunk 55 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 78 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 577 GLN ** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 724 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.162333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.134528 restraints weight = 65256.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.138039 restraints weight = 43369.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.137065 restraints weight = 32748.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.137388 restraints weight = 34184.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.137476 restraints weight = 31629.563| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6331 Z= 0.125 Angle : 0.451 6.963 8594 Z= 0.241 Chirality : 0.042 0.142 986 Planarity : 0.004 0.049 1116 Dihedral : 5.013 55.977 853 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.86 % Allowed : 24.48 % Favored : 71.66 % 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: 1.02 (0.31), residues: 790 helix: 1.94 (0.28), residues: 352 sheet: -0.13 (0.57), residues: 92 loop : -0.39 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 394 TYR 0.009 0.001 TYR B 796 PHE 0.013 0.001 PHE B 761 TRP 0.004 0.001 TRP B 689 HIS 0.001 0.000 HIS B 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 6330) covalent geometry : angle 0.45013 / 0.24 ( 8592) SS BOND : bond 0.00150 / 0.08 ( 1) SS BOND : angle 2.13860 / 1.15 ( 2) hydrogen bonds : bond 0.03692 / 2.37 ( 314) hydrogen bonds : angle 3.78805 / 2.54 ( 867) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 71 time to evaluate : 0.137 Fit side-chains revert: symmetry clash REVERT: B 78 GLU cc_start: 0.6677 (mm-30) cc_final: 0.6433 (tp30) REVERT: B 330 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.7101 (tptp) REVERT: B 427 ILE cc_start: 0.7207 (OUTLIER) cc_final: 0.6533 (pp) REVERT: B 577 GLN cc_start: 0.5970 (tp-100) cc_final: 0.5220 (tt0) REVERT: B 578 GLN cc_start: 0.8477 (mm-40) cc_final: 0.8222 (tp-100) REVERT: B 679 LYS cc_start: 0.5930 (mmpt) cc_final: 0.5314 (mmpt) outliers start: 26 outliers final: 13 residues processed: 92 average time/residue: 0.0587 time to fit residues: 7.3179 Evaluate side-chains 84 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 330 LYS Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 375 TYR Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 601 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 70 optimal weight: 0.2980 chunk 1 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 724 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.159618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.130982 restraints weight = 66321.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.134207 restraints weight = 45975.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.133152 restraints weight = 35850.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.133180 restraints weight = 37119.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.133319 restraints weight = 34683.823| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6331 Z= 0.162 Angle : 0.486 7.380 8594 Z= 0.259 Chirality : 0.043 0.148 986 Planarity : 0.004 0.049 1116 Dihedral : 5.163 54.959 853 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.45 % Allowed : 23.29 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.30), residues: 790 helix: 1.74 (0.28), residues: 353 sheet: -0.09 (0.58), residues: 92 loop : -0.48 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 394 TYR 0.010 0.001 TYR B 796 PHE 0.015 0.002 PHE B 761 TRP 0.011 0.002 TRP B 575 HIS 0.001 0.000 HIS B 512 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.16 ( 6330) covalent geometry : angle 0.48472 / 0.26 ( 8592) SS BOND : bond 0.00174 / 0.09 ( 1) SS BOND : angle 2.13811 / 1.15 ( 2) hydrogen bonds : bond 0.04032 / 2.58 ( 314) hydrogen bonds : angle 3.87620 / 2.62 ( 867) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 68 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: B 330 LYS cc_start: 0.7699 (OUTLIER) cc_final: 0.7077 (tptp) REVERT: B 349 GLN cc_start: 0.7666 (OUTLIER) cc_final: 0.6996 (mt0) REVERT: B 379 ASN cc_start: 0.7966 (OUTLIER) cc_final: 0.7165 (p0) REVERT: B 427 ILE cc_start: 0.7227 (OUTLIER) cc_final: 0.6547 (pp) REVERT: B 577 GLN cc_start: 0.5949 (tp-100) cc_final: 0.5224 (tt0) REVERT: B 578 GLN cc_start: 0.8403 (mm-40) cc_final: 0.8185 (tp-100) REVERT: B 679 LYS cc_start: 0.6064 (mmpt) cc_final: 0.5471 (mmpt) outliers start: 30 outliers final: 18 residues processed: 92 average time/residue: 0.0634 time to fit residues: 7.8937 Evaluate side-chains 86 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 64 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 274 ASN Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 330 LYS Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 375 TYR Chi-restraints excluded: chain B residue 379 ASN Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 646 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 42 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 69 optimal weight: 7.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 235 GLN ** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 724 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.159832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.133349 restraints weight = 67198.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.137297 restraints weight = 46192.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.135147 restraints weight = 33936.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.135561 restraints weight = 36230.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.135518 restraints weight = 33901.400| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6331 Z= 0.140 Angle : 0.465 6.516 8594 Z= 0.249 Chirality : 0.042 0.144 986 Planarity : 0.004 0.049 1116 Dihedral : 4.997 50.718 853 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.45 % Allowed : 23.74 % Favored : 71.81 % 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: 0.85 (0.30), residues: 790 helix: 1.79 (0.28), residues: 353 sheet: -0.12 (0.57), residues: 92 loop : -0.49 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 394 TYR 0.010 0.001 TYR B 796 PHE 0.013 0.001 PHE B 761 TRP 0.017 0.002 TRP B 575 HIS 0.001 0.000 HIS B 512 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 ( 6330) covalent geometry : angle 0.46435 / 0.25 ( 8592) SS BOND : bond 0.00136 / 0.07 ( 1) SS BOND : angle 2.08488 / 1.12 ( 2) hydrogen bonds : bond 0.03848 / 2.46 ( 314) hydrogen bonds : angle 3.80514 / 2.56 ( 867) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 69 time to evaluate : 0.146 Fit side-chains revert: symmetry clash REVERT: B 78 GLU cc_start: 0.6737 (mm-30) cc_final: 0.6514 (tp30) REVERT: B 330 LYS cc_start: 0.7760 (OUTLIER) cc_final: 0.7120 (tptp) REVERT: B 349 GLN cc_start: 0.7658 (OUTLIER) cc_final: 0.6914 (mt0) REVERT: B 379 ASN cc_start: 0.7977 (OUTLIER) cc_final: 0.7280 (p0) REVERT: B 427 ILE cc_start: 0.7100 (OUTLIER) cc_final: 0.6438 (pp) REVERT: B 578 GLN cc_start: 0.8323 (mm-40) cc_final: 0.8119 (tp-100) REVERT: B 679 LYS cc_start: 0.6055 (mmpt) cc_final: 0.4862 (ttpt) outliers start: 30 outliers final: 17 residues processed: 93 average time/residue: 0.0645 time to fit residues: 8.0333 Evaluate side-chains 86 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 274 ASN Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 330 LYS Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 375 TYR Chi-restraints excluded: chain B residue 379 ASN Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 819 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 11 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 235 GLN B 588 ASN ** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 724 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.160674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.132679 restraints weight = 67061.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.137270 restraints weight = 43737.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.135191 restraints weight = 33264.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.135262 restraints weight = 34198.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.135263 restraints weight = 33416.379| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6331 Z= 0.133 Angle : 0.462 7.465 8594 Z= 0.247 Chirality : 0.042 0.143 986 Planarity : 0.004 0.048 1116 Dihedral : 4.375 31.358 849 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.71 % Allowed : 24.18 % Favored : 72.11 % 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: 0.89 (0.31), residues: 790 helix: 1.81 (0.28), residues: 353 sheet: -0.11 (0.58), residues: 92 loop : -0.46 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 394 TYR 0.009 0.001 TYR B 796 PHE 0.013 0.001 PHE B 761 TRP 0.019 0.002 TRP B 575 HIS 0.001 0.000 HIS B 512 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.13 ( 6330) covalent geometry : angle 0.46076 / 0.25 ( 8592) SS BOND : bond 0.00113 / 0.06 ( 1) SS BOND : angle 2.05106 / 1.10 ( 2) hydrogen bonds : bond 0.03760 / 2.40 ( 314) hydrogen bonds : angle 3.79965 / 2.56 ( 867) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 71 time to evaluate : 0.133 Fit side-chains revert: symmetry clash REVERT: B 78 GLU cc_start: 0.6720 (mm-30) cc_final: 0.6467 (tp30) REVERT: B 330 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.7068 (tptp) REVERT: B 349 GLN cc_start: 0.7646 (OUTLIER) cc_final: 0.6928 (mt0) REVERT: B 379 ASN cc_start: 0.8027 (OUTLIER) cc_final: 0.7328 (p0) REVERT: B 427 ILE cc_start: 0.7185 (OUTLIER) cc_final: 0.6504 (pp) REVERT: B 578 GLN cc_start: 0.8329 (mm-40) cc_final: 0.8128 (tp-100) REVERT: B 679 LYS cc_start: 0.5848 (mmpt) cc_final: 0.4779 (ttpt) outliers start: 25 outliers final: 17 residues processed: 91 average time/residue: 0.0577 time to fit residues: 7.0811 Evaluate side-chains 86 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 274 ASN Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 330 LYS Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 375 TYR Chi-restraints excluded: chain B residue 379 ASN Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 819 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 69 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 chunk 77 optimal weight: 0.3980 chunk 70 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 235 GLN ** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 724 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.160160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.131515 restraints weight = 66829.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.134064 restraints weight = 46519.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.133299 restraints weight = 36306.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.133893 restraints weight = 38282.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.134245 restraints weight = 34344.756| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6331 Z= 0.151 Angle : 0.478 6.939 8594 Z= 0.255 Chirality : 0.042 0.145 986 Planarity : 0.004 0.049 1116 Dihedral : 4.433 32.133 849 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.86 % Allowed : 24.93 % Favored : 71.22 % 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: 0.82 (0.30), residues: 790 helix: 1.74 (0.28), residues: 353 sheet: -0.09 (0.60), residues: 84 loop : -0.50 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 394 TYR 0.010 0.001 TYR B 796 PHE 0.015 0.001 PHE B 761 TRP 0.021 0.002 TRP B 575 HIS 0.001 0.000 HIS B 512 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.15 ( 6330) covalent geometry : angle 0.47686 / 0.25 ( 8592) SS BOND : bond 0.00123 / 0.06 ( 1) SS BOND : angle 2.05455 / 1.10 ( 2) hydrogen bonds : bond 0.03908 / 2.49 ( 314) hydrogen bonds : angle 3.83364 / 2.58 ( 867) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 67 time to evaluate : 0.148 Fit side-chains revert: symmetry clash REVERT: B 78 GLU cc_start: 0.6752 (mm-30) cc_final: 0.6493 (tp30) REVERT: B 330 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7221 (tptp) REVERT: B 349 GLN cc_start: 0.7680 (OUTLIER) cc_final: 0.6905 (mt0) REVERT: B 379 ASN cc_start: 0.8028 (OUTLIER) cc_final: 0.7291 (p0) REVERT: B 427 ILE cc_start: 0.7212 (OUTLIER) cc_final: 0.6524 (pp) REVERT: B 679 LYS cc_start: 0.6081 (mmpt) cc_final: 0.4900 (ttpt) outliers start: 26 outliers final: 18 residues processed: 89 average time/residue: 0.0602 time to fit residues: 7.2071 Evaluate side-chains 89 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 274 ASN Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 330 LYS Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 375 TYR Chi-restraints excluded: chain B residue 379 ASN Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 819 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 73 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 724 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.160097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.132555 restraints weight = 67024.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.136727 restraints weight = 45796.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.134902 restraints weight = 33969.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.135220 restraints weight = 35850.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.135451 restraints weight = 33631.287| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6331 Z= 0.137 Angle : 0.474 7.416 8594 Z= 0.253 Chirality : 0.042 0.147 986 Planarity : 0.004 0.048 1116 Dihedral : 4.350 30.670 849 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.41 % Allowed : 25.07 % Favored : 71.51 % 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: 0.84 (0.30), residues: 790 helix: 1.80 (0.28), residues: 353 sheet: -0.16 (0.57), residues: 92 loop : -0.53 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 394 TYR 0.009 0.001 TYR B 796 PHE 0.013 0.001 PHE B 761 TRP 0.025 0.003 TRP B 575 HIS 0.001 0.000 HIS B 512 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 6330) covalent geometry : angle 0.47331 / 0.25 ( 8592) SS BOND : bond 0.00174 / 0.09 ( 1) SS BOND : angle 2.14076 / 1.14 ( 2) hydrogen bonds : bond 0.03765 / 2.40 ( 314) hydrogen bonds : angle 3.78004 / 2.54 ( 867) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 0.144 Fit side-chains revert: symmetry clash REVERT: B 78 GLU cc_start: 0.6809 (mm-30) cc_final: 0.6549 (tp30) REVERT: B 330 LYS cc_start: 0.7736 (OUTLIER) cc_final: 0.7091 (tptp) REVERT: B 349 GLN cc_start: 0.7688 (OUTLIER) cc_final: 0.6957 (mt0) REVERT: B 379 ASN cc_start: 0.8033 (OUTLIER) cc_final: 0.7304 (p0) REVERT: B 427 ILE cc_start: 0.7099 (OUTLIER) cc_final: 0.6531 (pp) REVERT: B 679 LYS cc_start: 0.5909 (mmpt) cc_final: 0.4828 (ttpt) outliers start: 23 outliers final: 17 residues processed: 90 average time/residue: 0.0600 time to fit residues: 7.2268 Evaluate side-chains 90 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 274 ASN Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 330 LYS Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 375 TYR Chi-restraints excluded: chain B residue 379 ASN Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 601 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 16 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 69 optimal weight: 7.9990 chunk 50 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 66 optimal weight: 0.4980 chunk 30 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 235 GLN B 578 GLN ** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 724 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.159458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.132382 restraints weight = 66150.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.135653 restraints weight = 46335.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.134607 restraints weight = 34587.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.134775 restraints weight = 33997.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.134728 restraints weight = 33064.447| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6331 Z= 0.149 Angle : 0.486 7.489 8594 Z= 0.259 Chirality : 0.042 0.149 986 Planarity : 0.004 0.049 1116 Dihedral : 4.409 31.340 849 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.26 % Allowed : 25.52 % Favored : 71.22 % 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: 0.78 (0.30), residues: 790 helix: 1.74 (0.28), residues: 353 sheet: -0.17 (0.57), residues: 92 loop : -0.56 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 394 TYR 0.010 0.001 TYR B 796 PHE 0.020 0.002 PHE B 436 TRP 0.028 0.003 TRP B 575 HIS 0.001 0.000 HIS B 512 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 ( 6330) covalent geometry : angle 0.48491 / 0.26 ( 8592) SS BOND : bond 0.00161 / 0.08 ( 1) SS BOND : angle 2.12692 / 1.13 ( 2) hydrogen bonds : bond 0.03878 / 2.48 ( 314) hydrogen bonds : angle 3.80791 / 2.56 ( 867) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 0.137 Fit side-chains revert: symmetry clash REVERT: B 78 GLU cc_start: 0.6776 (mm-30) cc_final: 0.6512 (tp30) REVERT: B 330 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7140 (tptp) REVERT: B 349 GLN cc_start: 0.7689 (OUTLIER) cc_final: 0.6980 (mt0) REVERT: B 379 ASN cc_start: 0.7978 (OUTLIER) cc_final: 0.7165 (p0) REVERT: B 427 ILE cc_start: 0.7205 (OUTLIER) cc_final: 0.6484 (pp) REVERT: B 679 LYS cc_start: 0.6058 (mmpt) cc_final: 0.4910 (ttpt) outliers start: 22 outliers final: 18 residues processed: 90 average time/residue: 0.0610 time to fit residues: 7.2685 Evaluate side-chains 91 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 69 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 274 ASN Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 330 LYS Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 375 TYR Chi-restraints excluded: chain B residue 379 ASN Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 819 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 75 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 724 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.159988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.132518 restraints weight = 67121.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.136204 restraints weight = 47789.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.134555 restraints weight = 35843.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.134611 restraints weight = 36100.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.134703 restraints weight = 34072.505| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6331 Z= 0.138 Angle : 0.479 7.573 8594 Z= 0.256 Chirality : 0.042 0.148 986 Planarity : 0.004 0.048 1116 Dihedral : 4.361 30.162 849 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.41 % Allowed : 25.37 % Favored : 71.22 % 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: 0.82 (0.31), residues: 790 helix: 1.81 (0.28), residues: 353 sheet: -0.17 (0.57), residues: 92 loop : -0.55 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 394 TYR 0.009 0.001 TYR B 796 PHE 0.013 0.001 PHE B 761 TRP 0.027 0.003 TRP B 575 HIS 0.001 0.000 HIS B 512 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 ( 6330) covalent geometry : angle 0.47799 / 0.26 ( 8592) SS BOND : bond 0.00175 / 0.09 ( 1) SS BOND : angle 2.14801 / 1.14 ( 2) hydrogen bonds : bond 0.03762 / 2.40 ( 314) hydrogen bonds : angle 3.77083 / 2.54 ( 867) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 808.83 seconds wall clock time: 14 minutes 35.99 seconds (875.99 seconds total)