Starting phenix.real_space_refine on Mon Oct 26 06:36:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11am_75590/10_2026/11am_75590.cif Found real_map, /net/cci-nas-00/data/ceres_data/11am_75590/10_2026/11am_75590.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/11am_75590/10_2026/11am_75590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11am_75590/10_2026/11am_75590.map" model { file = "/net/cci-nas-00/data/ceres_data/11am_75590/10_2026/11am_75590.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11am_75590/10_2026/11am_75590.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.023 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: 6 Type Number sf(0) Gaussians S 50 5.16 5 Cl 2 4.86 5 C 6290 2.51 5 N 1556 2.21 5 O 1692 1.98 5 H 9718 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19308 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 9653 Classifications: {'peptide': 621} Link IDs: {'PTRANS': 33, 'TRANS': 587} Chain breaks: 2 Chain: "B" Number of atoms: 9653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 9653 Classifications: {'peptide': 621} Link IDs: {'PTRANS': 33, 'TRANS': 587} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.33, per 1000 atoms: 0.17 Number of scatterers: 19308 At special positions: 0 Unit cell: (79.287, 110.409, 113.373, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 2 17.00 S 50 16.00 O 1692 8.00 N 1556 7.00 C 6290 6.00 H 9718 1.00 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: 1.68 Conformation dependent library (CDL) restraints added in 578.8 milliseconds 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2316 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 6 sheets defined 70.7% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 49 through 85 Processing helix chain 'A' and resid 88 through 113 removed outlier: 4.225A pdb=" N TYR A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) Proline residue: A 100 - end of helix removed outlier: 3.901A pdb=" N SER A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 130 Processing helix chain 'A' and resid 135 through 141 removed outlier: 3.850A pdb=" N ASP A 140 " --> pdb=" O ASP A 137 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE A 141 " --> pdb=" O TYR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 156 removed outlier: 4.748A pdb=" N ALA A 146 " --> pdb=" O LYS A 142 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS A 147 " --> pdb=" O ASN A 143 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL A 149 " --> pdb=" O GLY A 145 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY A 150 " --> pdb=" O ALA A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.836A pdb=" N THR A 160 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE A 161 " --> pdb=" O GLY A 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 157 through 161' Processing helix chain 'A' and resid 165 through 188 Processing helix chain 'A' and resid 193 through 214 removed outlier: 3.621A pdb=" N MET A 200 " --> pdb=" O LYS A 196 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL A 212 " --> pdb=" O GLY A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 228 removed outlier: 3.761A pdb=" N SER A 228 " --> pdb=" O ILE A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 257 Processing helix chain 'A' and resid 280 through 313 removed outlier: 4.234A pdb=" N PHE A 284 " --> pdb=" O PRO A 280 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N CYS A 297 " --> pdb=" O GLY A 293 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS A 311 " --> pdb=" O LEU A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 323 removed outlier: 3.629A pdb=" N SER A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 338 Processing helix chain 'A' and resid 353 through 362 removed outlier: 3.958A pdb=" N LEU A 358 " --> pdb=" O MET A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 374 removed outlier: 3.677A pdb=" N LEU A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 392 removed outlier: 4.326A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N TRP A 388 " --> pdb=" O GLN A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 417 removed outlier: 3.829A pdb=" N TRP A 411 " --> pdb=" O VAL A 407 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE A 414 " --> pdb=" O PHE A 410 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 415 " --> pdb=" O TRP A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 448 removed outlier: 4.082A pdb=" N ILE A 429 " --> pdb=" O TYR A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 480 removed outlier: 4.042A pdb=" N TYR A 466 " --> pdb=" O MET A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 493 Processing helix chain 'A' and resid 497 through 513 removed outlier: 3.786A pdb=" N VAL A 501 " --> pdb=" O HIS A 497 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE A 511 " --> pdb=" O ALA A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 528 removed outlier: 3.581A pdb=" N THR A 523 " --> pdb=" O PHE A 519 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL A 526 " --> pdb=" O GLY A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 551 removed outlier: 3.875A pdb=" N PHE A 550 " --> pdb=" O THR A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 575 removed outlier: 3.940A pdb=" N ASP A 575 " --> pdb=" O VAL A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 605 Processing helix chain 'A' and resid 619 through 625 Processing helix chain 'A' and resid 640 through 652 Processing helix chain 'A' and resid 670 through 682 Processing helix chain 'B' and resid 49 through 85 Processing helix chain 'B' and resid 88 through 113 removed outlier: 4.225A pdb=" N TYR B 99 " --> pdb=" O SER B 95 " (cutoff:3.500A) Proline residue: B 100 - end of helix removed outlier: 3.901A pdb=" N SER B 113 " --> pdb=" O GLY B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 130 Processing helix chain 'B' and resid 135 through 141 removed outlier: 3.850A pdb=" N ASP B 140 " --> pdb=" O ASP B 137 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE B 141 " --> pdb=" O TYR B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 156 removed outlier: 4.748A pdb=" N ALA B 146 " --> pdb=" O LYS B 142 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS B 147 " --> pdb=" O ASN B 143 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL B 149 " --> pdb=" O GLY B 145 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY B 150 " --> pdb=" O ALA B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 161 removed outlier: 3.836A pdb=" N THR B 160 " --> pdb=" O SER B 157 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE B 161 " --> pdb=" O GLY B 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 157 through 161' Processing helix chain 'B' and resid 165 through 188 Processing helix chain 'B' and resid 193 through 214 removed outlier: 3.621A pdb=" N MET B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL B 212 " --> pdb=" O GLY B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 228 removed outlier: 3.761A pdb=" N SER B 228 " --> pdb=" O ILE B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 257 Processing helix chain 'B' and resid 280 through 313 removed outlier: 4.235A pdb=" N PHE B 284 " --> pdb=" O PRO B 280 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N CYS B 297 " --> pdb=" O GLY B 293 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS B 311 " --> pdb=" O LEU B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 323 removed outlier: 3.629A pdb=" N SER B 323 " --> pdb=" O LEU B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 338 Processing helix chain 'B' and resid 353 through 362 removed outlier: 3.957A pdb=" N LEU B 358 " --> pdb=" O MET B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 374 removed outlier: 3.677A pdb=" N LEU B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG B 372 " --> pdb=" O ALA B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 392 removed outlier: 4.326A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N TRP B 388 " --> pdb=" O GLN B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 417 removed outlier: 3.829A pdb=" N TRP B 411 " --> pdb=" O VAL B 407 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE B 414 " --> pdb=" O PHE B 410 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU B 415 " --> pdb=" O TRP B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 448 removed outlier: 4.080A pdb=" N ILE B 429 " --> pdb=" O TYR B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 480 removed outlier: 4.041A pdb=" N TYR B 466 " --> pdb=" O MET B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 493 Processing helix chain 'B' and resid 497 through 513 removed outlier: 3.786A pdb=" N VAL B 501 " --> pdb=" O HIS B 497 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE B 511 " --> pdb=" O ALA B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 528 removed outlier: 3.572A pdb=" N THR B 523 " --> pdb=" O PHE B 519 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL B 526 " --> pdb=" O GLY B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 551 removed outlier: 3.875A pdb=" N PHE B 550 " --> pdb=" O THR B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 575 removed outlier: 3.940A pdb=" N ASP B 575 " --> pdb=" O VAL B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 605 Processing helix chain 'B' and resid 619 through 625 Processing helix chain 'B' and resid 640 through 652 Processing helix chain 'B' and resid 670 through 682 Processing sheet with id=AA1, first strand: chain 'A' and resid 230 through 232 removed outlier: 4.403A pdb=" N PHE A 231 " --> pdb=" O PHE B 231 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N PHE B 231 " --> pdb=" O PHE A 231 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 558 through 559 removed outlier: 6.367A pdb=" N LEU A 558 " --> pdb=" O VAL A 582 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 633 through 635 Processing sheet with id=AA4, first strand: chain 'A' and resid 655 through 660 removed outlier: 6.604A pdb=" N SER A 660 " --> pdb=" O ALA A 664 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N ALA A 664 " --> pdb=" O SER A 660 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 558 through 559 removed outlier: 6.367A pdb=" N LEU B 558 " --> pdb=" O VAL B 582 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 655 through 660 removed outlier: 6.604A pdb=" N SER B 660 " --> pdb=" O ALA B 664 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N ALA B 664 " --> pdb=" O SER B 660 " (cutoff:3.500A) 604 hydrogen bonds defined for protein. 1770 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: 4.27 Time building geometry restraints manager: 2.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8194 1.03 - 1.23: 1531 1.23 - 1.42: 4385 1.42 - 1.61: 5368 1.61 - 1.81: 84 Bond restraints: 19562 Sorted by residual: bond pdb=" CE1 HIS A 171 " pdb=" NE2 HIS A 171 " ideal model delta sigma weight residual 1.321 1.229 0.092 1.00e-02 1.00e+04 8.37e+01 bond pdb=" CE1 HIS B 480 " pdb=" NE2 HIS B 480 " ideal model delta sigma weight residual 1.321 1.231 0.090 1.00e-02 1.00e+04 8.13e+01 bond pdb=" CE1 HIS B 171 " pdb=" NE2 HIS B 171 " ideal model delta sigma weight residual 1.321 1.231 0.090 1.00e-02 1.00e+04 8.13e+01 bond pdb=" CE1 HIS A 480 " pdb=" NE2 HIS A 480 " ideal model delta sigma weight residual 1.321 1.231 0.090 1.00e-02 1.00e+04 8.12e+01 bond pdb=" CD2 HIS A 480 " pdb=" NE2 HIS A 480 " ideal model delta sigma weight residual 1.374 1.282 0.092 1.10e-02 8.26e+03 7.06e+01 ... (remaining 19557 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 31043 2.04 - 4.08: 2801 4.08 - 6.12: 1030 6.12 - 8.16: 507 8.16 - 10.21: 35 Bond angle restraints: 35416 Sorted by residual: angle pdb=" CA PHE B 162 " pdb=" CB PHE B 162 " pdb=" CG PHE B 162 " ideal model delta sigma weight residual 113.80 120.86 -7.06 1.00e+00 1.00e+00 4.98e+01 angle pdb=" CA PHE A 162 " pdb=" CB PHE A 162 " pdb=" CG PHE A 162 " ideal model delta sigma weight residual 113.80 120.86 -7.06 1.00e+00 1.00e+00 4.98e+01 angle pdb=" CA PHE A 430 " pdb=" CB PHE A 430 " pdb=" CG PHE A 430 " ideal model delta sigma weight residual 113.80 120.59 -6.79 1.00e+00 1.00e+00 4.60e+01 angle pdb=" CA PHE B 430 " pdb=" CB PHE B 430 " pdb=" CG PHE B 430 " ideal model delta sigma weight residual 113.80 120.56 -6.76 1.00e+00 1.00e+00 4.57e+01 angle pdb=" CA PHE B 213 " pdb=" CB PHE B 213 " pdb=" CG PHE B 213 " ideal model delta sigma weight residual 113.80 120.40 -6.60 1.00e+00 1.00e+00 4.36e+01 ... (remaining 35411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.82: 8204 15.82 - 31.64: 700 31.64 - 47.46: 232 47.46 - 63.28: 126 63.28 - 79.11: 20 Dihedral angle restraints: 9282 sinusoidal: 4894 harmonic: 4388 Sorted by residual: dihedral pdb=" C VAL A 526 " pdb=" N VAL A 526 " pdb=" CA VAL A 526 " pdb=" CB VAL A 526 " ideal model delta harmonic sigma weight residual -122.00 -134.56 12.56 0 2.50e+00 1.60e-01 2.53e+01 dihedral pdb=" N ILE A 161 " pdb=" C ILE A 161 " pdb=" CA ILE A 161 " pdb=" CB ILE A 161 " ideal model delta harmonic sigma weight residual 123.40 135.88 -12.48 0 2.50e+00 1.60e-01 2.49e+01 dihedral pdb=" C VAL B 526 " pdb=" N VAL B 526 " pdb=" CA VAL B 526 " pdb=" CB VAL B 526 " ideal model delta harmonic sigma weight residual -122.00 -134.47 12.47 0 2.50e+00 1.60e-01 2.49e+01 ... (remaining 9279 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 1277 0.129 - 0.257: 6 0.257 - 0.386: 8 0.386 - 0.515: 99 0.515 - 0.643: 170 Chirality restraints: 1560 Sorted by residual: chirality pdb=" CB THR A 484 " pdb=" CA THR A 484 " pdb=" OG1 THR A 484 " pdb=" CG2 THR A 484 " both_signs ideal model delta sigma weight residual False 2.55 1.91 0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" CB THR B 484 " pdb=" CA THR B 484 " pdb=" OG1 THR B 484 " pdb=" CG2 THR B 484 " both_signs ideal model delta sigma weight residual False 2.55 1.91 0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" CB VAL A 227 " pdb=" CA VAL A 227 " pdb=" CG1 VAL A 227 " pdb=" CG2 VAL A 227 " both_signs ideal model delta sigma weight residual False -2.63 -1.99 -0.64 2.00e-01 2.50e+01 1.02e+01 ... (remaining 1557 not shown) Planarity restraints: 2836 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 424 " -0.021 2.00e-02 2.50e+03 3.80e-02 1.44e+01 pdb=" N TYR B 425 " 0.066 2.00e-02 2.50e+03 pdb=" CA TYR B 425 " -0.019 2.00e-02 2.50e+03 pdb=" H TYR B 425 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 424 " 0.020 2.00e-02 2.50e+03 3.60e-02 1.29e+01 pdb=" N TYR A 425 " -0.062 2.00e-02 2.50e+03 pdb=" CA TYR A 425 " 0.018 2.00e-02 2.50e+03 pdb=" H TYR A 425 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 519 " -0.037 2.00e-02 2.50e+03 1.61e-02 7.76e+00 pdb=" CG PHE A 519 " 0.005 2.00e-02 2.50e+03 pdb=" CD1 PHE A 519 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 519 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE A 519 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 519 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 519 " -0.008 2.00e-02 2.50e+03 pdb=" HD1 PHE A 519 " 0.002 2.00e-02 2.50e+03 pdb=" HD2 PHE A 519 " 0.023 2.00e-02 2.50e+03 pdb=" HE1 PHE A 519 " 0.014 2.00e-02 2.50e+03 pdb=" HE2 PHE A 519 " -0.011 2.00e-02 2.50e+03 pdb=" HZ PHE A 519 " -0.020 2.00e-02 2.50e+03 ... (remaining 2833 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.37: 6379 2.37 - 2.93: 43539 2.93 - 3.48: 49996 3.48 - 4.04: 65691 4.04 - 4.60: 99414 Nonbonded interactions: 265019 Sorted by model distance: nonbonded pdb=" H GLY A 164 " pdb=" O GLY A 424 " model vdw 1.812 2.450 nonbonded pdb=" H GLY B 164 " pdb=" O GLY B 424 " model vdw 1.831 2.450 nonbonded pdb=" HG SER B 366 " pdb=" HG SER B 445 " model vdw 1.866 2.100 nonbonded pdb=" HG SER A 366 " pdb=" HG SER A 445 " model vdw 1.866 2.100 nonbonded pdb=" H LYS A 142 " pdb=" HG2 LYS A 142 " model vdw 1.882 2.270 ... (remaining 265014 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 6.260 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: 0.030 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.170 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 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 : 0.021 0.107 9844 Z= 1.164 Angle : 1.663 10.205 13410 Z= 1.099 Chirality : 0.228 0.643 1560 Planarity : 0.005 0.037 1666 Dihedral : 13.598 73.008 3434 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.17 % Allowed : 8.95 % Favored : 89.88 % Cbeta Deviations : 8.89 % 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: 0.15 (0.24), residues: 1230 helix: 0.81 (0.19), residues: 790 sheet: None (None), residues: 0 loop : -1.14 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 76 TYR 0.027 0.004 TYR A 299 PHE 0.026 0.004 PHE B 169 TRP 0.009 0.001 TRP B 534 HIS 0.004 0.001 HIS A 78 Details of bonding type rmsd/Z covalent geometry : bond 0.02131 / 1.16 ( 9844) covalent geometry : angle 1.66296 / 1.10 (13410) hydrogen bonds : bond 0.17135 / 10.74 ( 604) hydrogen bonds : angle 6.63984 / 4.76 ( 1770) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7816 (mp0) REVERT: B 442 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7803 (mp0) outliers start: 12 outliers final: 4 residues processed: 85 average time/residue: 0.1438 time to fit residues: 19.8708 Evaluate side-chains 64 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain B residue 665 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: [108, 49, 97, 113, 53, 5, 33, 123, 65, 62, 51] chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 123 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.104408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.079022 restraints weight = 63379.574| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 3.20 r_work: 0.2994 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9844 Z= 0.119 Angle : 0.491 4.710 13410 Z= 0.258 Chirality : 0.035 0.121 1560 Planarity : 0.004 0.033 1666 Dihedral : 4.919 59.631 1328 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.97 % Allowed : 10.31 % Favored : 88.72 % 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: 1.42 (0.24), residues: 1230 helix: 1.91 (0.19), residues: 792 sheet: None (None), residues: 0 loop : -0.88 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 304 TYR 0.010 0.001 TYR B 99 PHE 0.009 0.001 PHE B 667 TRP 0.008 0.001 TRP A 388 HIS 0.003 0.001 HIS B 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 ( 9844) covalent geometry : angle 0.49080 / 0.26 (13410) hydrogen bonds : bond 0.05330 / 3.50 ( 604) hydrogen bonds : angle 4.66219 / 3.40 ( 1770) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.6562 (mpt) REVERT: A 442 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7186 (mp0) REVERT: B 408 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.6557 (mpt) REVERT: B 442 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7197 (mp0) outliers start: 10 outliers final: 4 residues processed: 69 average time/residue: 0.1440 time to fit residues: 16.0222 Evaluate side-chains 68 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 665 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: [97, 98, 79, 49, 11, 24, 68, 100, 111, 7, 40] chunk 97 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 chunk 100 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.101846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.076296 restraints weight = 64708.762| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 3.22 r_work: 0.2947 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 9844 Z= 0.173 Angle : 0.506 4.852 13410 Z= 0.269 Chirality : 0.036 0.124 1560 Planarity : 0.004 0.036 1666 Dihedral : 4.535 56.093 1324 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.97 % Allowed : 11.09 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.25), residues: 1230 helix: 2.25 (0.19), residues: 802 sheet: None (None), residues: 0 loop : -1.21 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 538 TYR 0.012 0.001 TYR B 99 PHE 0.013 0.001 PHE B 667 TRP 0.009 0.001 TRP B 388 HIS 0.004 0.001 HIS A 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 ( 9844) covalent geometry : angle 0.50650 / 0.27 (13410) hydrogen bonds : bond 0.05211 / 3.47 ( 604) hydrogen bonds : angle 4.38033 / 3.21 ( 1770) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.7995 (OUTLIER) cc_final: 0.6484 (mpt) REVERT: A 442 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7020 (mp0) REVERT: B 408 MET cc_start: 0.7999 (OUTLIER) cc_final: 0.6488 (mpt) REVERT: B 442 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7036 (mp0) outliers start: 10 outliers final: 6 residues processed: 70 average time/residue: 0.1452 time to fit residues: 16.6871 Evaluate side-chains 72 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 665 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: [38, 45, 118, 20, 52, 102, 120, 68, 13, 96, 34] chunk 38 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 118 optimal weight: 0.0970 chunk 20 optimal weight: 5.9990 chunk 52 optimal weight: 20.0000 chunk 102 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.101599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.076277 restraints weight = 64417.985| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 3.19 r_work: 0.2948 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9844 Z= 0.158 Angle : 0.487 4.907 13410 Z= 0.258 Chirality : 0.036 0.122 1560 Planarity : 0.004 0.035 1666 Dihedral : 4.417 54.559 1324 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.46 % Allowed : 11.67 % Favored : 86.87 % 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: 1.80 (0.25), residues: 1230 helix: 2.38 (0.19), residues: 808 sheet: None (None), residues: 0 loop : -1.26 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 538 TYR 0.012 0.001 TYR A 99 PHE 0.013 0.001 PHE A 217 TRP 0.008 0.001 TRP B 388 HIS 0.004 0.001 HIS B 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 ( 9844) covalent geometry : angle 0.48686 / 0.26 (13410) hydrogen bonds : bond 0.04877 / 3.27 ( 604) hydrogen bonds : angle 4.21618 / 3.09 ( 1770) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.6482 (mpt) REVERT: A 442 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.6963 (mp0) REVERT: B 408 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.6462 (mpt) REVERT: B 442 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.6979 (mp0) outliers start: 15 outliers final: 9 residues processed: 75 average time/residue: 0.1377 time to fit residues: 16.7806 Evaluate side-chains 75 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 665 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: [111, 79, 114, 31, 24, 94, 88, 43, 34, 65, 70] chunk 111 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 114 optimal weight: 20.0000 chunk 31 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.103890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.079751 restraints weight = 64615.239| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 3.00 r_work: 0.3079 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 9844 Z= 0.187 Angle : 0.507 4.952 13410 Z= 0.271 Chirality : 0.037 0.124 1560 Planarity : 0.004 0.035 1666 Dihedral : 4.398 52.848 1324 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.04 % Allowed : 11.19 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.24), residues: 1230 helix: 2.40 (0.18), residues: 808 sheet: None (None), residues: 0 loop : -1.37 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 538 TYR 0.013 0.001 TYR B 99 PHE 0.018 0.001 PHE A 217 TRP 0.009 0.001 TRP A 534 HIS 0.004 0.001 HIS A 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.19 ( 9844) covalent geometry : angle 0.50707 / 0.27 (13410) hydrogen bonds : bond 0.05128 / 3.44 ( 604) hydrogen bonds : angle 4.25151 / 3.13 ( 1770) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 60 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 PHE cc_start: 0.5225 (p90) cc_final: 0.5013 (p90) REVERT: A 249 MET cc_start: 0.8872 (tpt) cc_final: 0.8501 (tpp) REVERT: A 408 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.6911 (mpt) REVERT: A 442 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7274 (mp0) REVERT: B 249 MET cc_start: 0.8866 (tpt) cc_final: 0.8501 (tpp) REVERT: B 408 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.6927 (mpt) REVERT: B 442 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7288 (mp0) outliers start: 21 outliers final: 13 residues processed: 77 average time/residue: 0.1776 time to fit residues: 21.0103 Evaluate side-chains 77 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 665 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: [90, 11, 61, 94, 12, 65, 52, 36, 43, 95, 110] chunk 90 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 52 optimal weight: 20.0000 chunk 36 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.102246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.076840 restraints weight = 64285.213| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 3.18 r_work: 0.2975 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9844 Z= 0.156 Angle : 0.485 4.921 13410 Z= 0.255 Chirality : 0.036 0.122 1560 Planarity : 0.004 0.034 1666 Dihedral : 4.331 52.221 1324 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.65 % Allowed : 11.96 % Favored : 86.38 % 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: 1.85 (0.25), residues: 1230 helix: 2.48 (0.18), residues: 808 sheet: None (None), residues: 0 loop : -1.40 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 538 TYR 0.012 0.001 TYR B 99 PHE 0.018 0.001 PHE A 217 TRP 0.008 0.001 TRP B 388 HIS 0.004 0.001 HIS A 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 9844) covalent geometry : angle 0.48486 / 0.26 (13410) hydrogen bonds : bond 0.04796 / 3.22 ( 604) hydrogen bonds : angle 4.14751 / 3.05 ( 1770) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 PHE cc_start: 0.5403 (p90) cc_final: 0.5158 (p90) REVERT: A 237 TRP cc_start: 0.8396 (m-10) cc_final: 0.6863 (t60) REVERT: A 249 MET cc_start: 0.8799 (tpt) cc_final: 0.8424 (tpp) REVERT: A 408 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.6692 (mpt) REVERT: A 442 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7180 (mp0) REVERT: B 237 TRP cc_start: 0.8391 (m-10) cc_final: 0.6869 (t60) REVERT: B 249 MET cc_start: 0.8787 (tpt) cc_final: 0.8420 (tpp) REVERT: B 408 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.6693 (mpt) REVERT: B 442 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7184 (mp0) outliers start: 17 outliers final: 13 residues processed: 77 average time/residue: 0.1437 time to fit residues: 18.1076 Evaluate side-chains 79 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 665 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: [43, 34, 115, 3, 116, 44, 45, 15, 117, 110, 37] chunk 43 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 117 optimal weight: 8.9990 chunk 110 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.101126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.075904 restraints weight = 64707.680| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 3.16 r_work: 0.2950 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 9844 Z= 0.204 Angle : 0.510 4.955 13410 Z= 0.273 Chirality : 0.037 0.125 1560 Planarity : 0.004 0.035 1666 Dihedral : 4.366 51.575 1324 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.04 % Allowed : 12.16 % Favored : 85.80 % 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: 1.76 (0.24), residues: 1230 helix: 2.43 (0.18), residues: 808 sheet: None (None), residues: 0 loop : -1.49 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 538 TYR 0.013 0.001 TYR B 99 PHE 0.018 0.002 PHE B 217 TRP 0.009 0.001 TRP B 388 HIS 0.004 0.001 HIS A 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.20 ( 9844) covalent geometry : angle 0.51042 / 0.27 (13410) hydrogen bonds : bond 0.05122 / 3.44 ( 604) hydrogen bonds : angle 4.24798 / 3.13 ( 1770) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 62 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 PHE cc_start: 0.5485 (p90) cc_final: 0.5155 (p90) REVERT: A 237 TRP cc_start: 0.8422 (m-10) cc_final: 0.6853 (t60) REVERT: A 249 MET cc_start: 0.8796 (tpt) cc_final: 0.8439 (tpp) REVERT: A 408 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.6661 (mpt) REVERT: A 442 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7256 (mp0) REVERT: B 237 TRP cc_start: 0.8414 (m-10) cc_final: 0.6864 (t60) REVERT: B 249 MET cc_start: 0.8794 (tpt) cc_final: 0.8442 (tpp) REVERT: B 408 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.6666 (mpt) REVERT: B 442 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7257 (mp0) outliers start: 21 outliers final: 15 residues processed: 81 average time/residue: 0.1647 time to fit residues: 20.9383 Evaluate side-chains 80 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 665 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: [6, 35, 116, 61, 81, 45, 27, 18, 75, 99, 43] chunk 6 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 116 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.102643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.077334 restraints weight = 64037.999| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 3.17 r_work: 0.2974 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9844 Z= 0.142 Angle : 0.476 5.521 13410 Z= 0.249 Chirality : 0.035 0.123 1560 Planarity : 0.003 0.034 1666 Dihedral : 4.273 51.345 1324 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.95 % Allowed : 12.65 % Favored : 85.41 % 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: 1.94 (0.25), residues: 1230 helix: 2.60 (0.18), residues: 806 sheet: None (None), residues: 0 loop : -1.44 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 538 TYR 0.012 0.001 TYR A 99 PHE 0.022 0.001 PHE A 217 TRP 0.009 0.001 TRP B 388 HIS 0.004 0.001 HIS A 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 ( 9844) covalent geometry : angle 0.47647 / 0.25 (13410) hydrogen bonds : bond 0.04666 / 3.14 ( 604) hydrogen bonds : angle 4.09059 / 3.01 ( 1770) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 62 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 PHE cc_start: 0.5489 (p90) cc_final: 0.5175 (p90) REVERT: A 237 TRP cc_start: 0.8394 (m-10) cc_final: 0.6839 (t60) REVERT: A 249 MET cc_start: 0.8808 (tpt) cc_final: 0.8448 (tpp) REVERT: A 408 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.6677 (mpt) REVERT: A 442 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7165 (mp0) REVERT: B 237 TRP cc_start: 0.8391 (m-10) cc_final: 0.6863 (t60) REVERT: B 249 MET cc_start: 0.8809 (tpt) cc_final: 0.8455 (tpp) REVERT: B 408 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.6696 (mpt) REVERT: B 442 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7167 (mp0) outliers start: 20 outliers final: 14 residues processed: 80 average time/residue: 0.1563 time to fit residues: 20.3162 Evaluate side-chains 79 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 665 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: [65, 13, 107, 89, 103, 54, 81, 87, 66, 24, 108] chunk 65 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.102991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.077787 restraints weight = 63671.365| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 3.16 r_work: 0.2987 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9844 Z= 0.126 Angle : 0.469 6.047 13410 Z= 0.243 Chirality : 0.035 0.125 1560 Planarity : 0.003 0.034 1666 Dihedral : 4.175 50.781 1324 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.75 % Allowed : 12.84 % Favored : 85.41 % 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: 2.08 (0.25), residues: 1230 helix: 2.68 (0.19), residues: 810 sheet: None (None), residues: 0 loop : -1.38 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 83 TYR 0.012 0.001 TYR A 99 PHE 0.023 0.001 PHE A 217 TRP 0.009 0.001 TRP B 388 HIS 0.003 0.001 HIS A 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 9844) covalent geometry : angle 0.46949 / 0.24 (13410) hydrogen bonds : bond 0.04403 / 2.96 ( 604) hydrogen bonds : angle 4.00072 / 2.94 ( 1770) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 PHE cc_start: 0.5471 (p90) cc_final: 0.5167 (p90) REVERT: A 237 TRP cc_start: 0.8354 (m-10) cc_final: 0.6832 (t60) REVERT: A 249 MET cc_start: 0.8802 (tpt) cc_final: 0.8438 (tpp) REVERT: A 408 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.6690 (mpt) REVERT: A 442 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7122 (mp0) REVERT: B 237 TRP cc_start: 0.8346 (m-10) cc_final: 0.6836 (t60) REVERT: B 249 MET cc_start: 0.8810 (tpt) cc_final: 0.8448 (tpp) REVERT: B 408 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.6700 (mpt) REVERT: B 442 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7128 (mp0) outliers start: 18 outliers final: 12 residues processed: 80 average time/residue: 0.1580 time to fit residues: 20.3418 Evaluate side-chains 77 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 665 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: [80, 35, 13, 71, 34, 10, 89, 119, 118, 1, 110] chunk 80 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 119 optimal weight: 0.0000 chunk 118 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.104270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.079007 restraints weight = 63865.220| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 3.16 r_work: 0.3016 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9844 Z= 0.099 Angle : 0.465 6.827 13410 Z= 0.235 Chirality : 0.035 0.128 1560 Planarity : 0.003 0.034 1666 Dihedral : 4.069 50.217 1324 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.26 % Allowed : 13.13 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.25), residues: 1230 helix: 2.83 (0.19), residues: 810 sheet: None (None), residues: 0 loop : -1.28 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 438 TYR 0.011 0.001 TYR A 99 PHE 0.022 0.001 PHE A 217 TRP 0.009 0.001 TRP B 388 HIS 0.003 0.000 HIS B 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 ( 9844) covalent geometry : angle 0.46523 / 0.23 (13410) hydrogen bonds : bond 0.03983 / 2.69 ( 604) hydrogen bonds : angle 3.87492 / 2.84 ( 1770) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 PHE cc_start: 0.5434 (p90) cc_final: 0.5176 (p90) REVERT: A 237 TRP cc_start: 0.8300 (m-10) cc_final: 0.6823 (t60) REVERT: A 249 MET cc_start: 0.8817 (tpt) cc_final: 0.8447 (tpp) REVERT: A 408 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.6698 (mpt) REVERT: A 442 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7066 (mp0) REVERT: B 237 TRP cc_start: 0.8307 (m-10) cc_final: 0.6852 (t60) REVERT: B 249 MET cc_start: 0.8824 (tpt) cc_final: 0.8457 (tpp) REVERT: B 408 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.6718 (mpt) REVERT: B 442 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7071 (mp0) outliers start: 13 outliers final: 8 residues processed: 75 average time/residue: 0.1487 time to fit residues: 18.2545 Evaluate side-chains 70 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 665 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: [35, 117, 100, 65, 13, 41, 16, 119, 88, 45, 30] chunk 35 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 chunk 100 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.103023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.077421 restraints weight = 64828.401| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 3.24 r_work: 0.2978 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9844 Z= 0.141 Angle : 0.482 6.879 13410 Z= 0.247 Chirality : 0.035 0.126 1560 Planarity : 0.004 0.035 1666 Dihedral : 4.080 49.353 1324 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.36 % Allowed : 13.13 % Favored : 85.51 % 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: 2.18 (0.25), residues: 1230 helix: 2.74 (0.19), residues: 810 sheet: None (None), residues: 0 loop : -1.31 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 83 TYR 0.012 0.001 TYR B 99 PHE 0.022 0.001 PHE A 217 TRP 0.008 0.001 TRP B 388 HIS 0.003 0.001 HIS B 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 ( 9844) covalent geometry : angle 0.48226 / 0.25 (13410) hydrogen bonds : bond 0.04325 / 2.91 ( 604) hydrogen bonds : angle 3.96475 / 2.91 ( 1770) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3598.04 seconds wall clock time: 61 minutes 49.08 seconds (3709.08 seconds total)