Starting phenix.real_space_refine on Fri Jul 3 00:26:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lgm_23327/07_2026/7lgm_23327.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lgm_23327/07_2026/7lgm_23327.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7lgm_23327/07_2026/7lgm_23327.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lgm_23327/07_2026/7lgm_23327.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lgm_23327/07_2026/7lgm_23327.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lgm_23327/07_2026/7lgm_23327.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7lgm_23327/07_2026/7lgm_23327.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lgm_23327/07_2026/7lgm_23327.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.053 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 46 5.16 5 C 6842 2.51 5 N 1942 2.21 5 O 2118 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-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10954 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5446 Classifications: {'peptide': 719} Link IDs: {'PTRANS': 25, 'TRANS': 693} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B Time building chain proxies: 4.36, per 1000 atoms: 0.40 Number of scatterers: 10954 At special positions: 0 Unit cell: (121.8, 138.04, 97.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 46 16.00 P 6 15.00 O 2118 8.00 N 1942 7.00 C 6842 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 429.9 milliseconds 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2608 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 14 sheets defined 37.7% alpha, 14.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 11 through 15 removed outlier: 4.605A pdb=" N VAL A 14 " --> pdb=" O GLY A 11 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N TYR A 15 " --> pdb=" O PRO A 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 11 through 15' Processing helix chain 'A' and resid 30 through 34 Processing helix chain 'A' and resid 40 through 50 removed outlier: 3.566A pdb=" N LYS A 48 " --> pdb=" O GLU A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 69 Processing helix chain 'A' and resid 75 through 84 Processing helix chain 'A' and resid 85 through 91 Processing helix chain 'A' and resid 121 through 136 Processing helix chain 'A' and resid 145 through 160 removed outlier: 3.653A pdb=" N ASP A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 175 removed outlier: 4.135A pdb=" N LEU A 169 " --> pdb=" O SER A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 218 Processing helix chain 'A' and resid 218 through 228 Processing helix chain 'A' and resid 246 through 251 Processing helix chain 'A' and resid 275 through 287 removed outlier: 4.010A pdb=" N ASP A 284 " --> pdb=" O GLU A 280 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE A 285 " --> pdb=" O ALA A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 340 Processing helix chain 'A' and resid 359 through 369 Processing helix chain 'A' and resid 405 through 420 Processing helix chain 'A' and resid 436 through 440 Processing helix chain 'A' and resid 452 through 456 removed outlier: 3.506A pdb=" N MET A 455 " --> pdb=" O GLY A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 473 Processing helix chain 'A' and resid 497 through 510 Processing helix chain 'A' and resid 535 through 544 Processing helix chain 'A' and resid 556 through 564 Processing helix chain 'A' and resid 593 through 603 removed outlier: 3.879A pdb=" N VAL A 600 " --> pdb=" O GLU A 596 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE A 601 " --> pdb=" O VAL A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 624 Processing helix chain 'A' and resid 645 through 649 Processing helix chain 'A' and resid 679 through 685 Proline residue: A 682 - end of helix Processing helix chain 'A' and resid 692 through 706 Processing helix chain 'A' and resid 710 through 719 Processing helix chain 'B' and resid 11 through 15 removed outlier: 4.606A pdb=" N VAL B 14 " --> pdb=" O GLY B 11 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TYR B 15 " --> pdb=" O PRO B 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 11 through 15' Processing helix chain 'B' and resid 30 through 34 Processing helix chain 'B' and resid 40 through 50 removed outlier: 3.567A pdb=" N LYS B 48 " --> pdb=" O GLU B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 69 Processing helix chain 'B' and resid 75 through 84 Processing helix chain 'B' and resid 85 through 91 Processing helix chain 'B' and resid 121 through 136 Processing helix chain 'B' and resid 145 through 160 removed outlier: 3.654A pdb=" N ASP B 149 " --> pdb=" O ASP B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 175 removed outlier: 4.135A pdb=" N LEU B 169 " --> pdb=" O SER B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 218 Processing helix chain 'B' and resid 218 through 228 Processing helix chain 'B' and resid 246 through 251 Processing helix chain 'B' and resid 275 through 287 removed outlier: 4.010A pdb=" N ASP B 284 " --> pdb=" O GLU B 280 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE B 285 " --> pdb=" O ALA B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 340 Processing helix chain 'B' and resid 359 through 369 Processing helix chain 'B' and resid 405 through 420 Processing helix chain 'B' and resid 436 through 440 Processing helix chain 'B' and resid 452 through 456 removed outlier: 3.505A pdb=" N MET B 455 " --> pdb=" O GLY B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 473 Processing helix chain 'B' and resid 497 through 510 Processing helix chain 'B' and resid 535 through 544 Processing helix chain 'B' and resid 556 through 564 Processing helix chain 'B' and resid 593 through 603 removed outlier: 3.879A pdb=" N VAL B 600 " --> pdb=" O GLU B 596 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ILE B 601 " --> pdb=" O VAL B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 645 through 649 Processing helix chain 'B' and resid 679 through 685 Proline residue: B 682 - end of helix Processing helix chain 'B' and resid 692 through 706 Processing helix chain 'B' and resid 710 through 719 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 9 removed outlier: 5.649A pdb=" N ILE A 3 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N VAL A 24 " --> pdb=" O ILE A 3 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU A 111 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ALA A 98 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N SER A 113 " --> pdb=" O GLY A 96 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 180 through 182 Processing sheet with id=AA3, first strand: chain 'A' and resid 270 through 273 removed outlier: 6.189A pdb=" N VAL A 256 " --> pdb=" O ASN A 272 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 313 through 318 removed outlier: 7.001A pdb=" N LEU A 307 " --> pdb=" O VAL A 314 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA A 316 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ARG A 305 " --> pdb=" O ALA A 316 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ARG A 318 " --> pdb=" O ASP A 303 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ASP A 303 " --> pdb=" O ARG A 318 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASP A 427 " --> pdb=" O CYS A 445 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 323 through 325 Processing sheet with id=AA6, first strand: chain 'A' and resid 526 through 527 removed outlier: 7.860A pdb=" N GLY A 514 " --> pdb=" O VAL A 552 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE A 486 " --> pdb=" O ALA A 551 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N LEU A 553 " --> pdb=" O ILE A 486 " (cutoff:3.500A) removed outlier: 9.642A pdb=" N ALA A 488 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ALA A 487 " --> pdb=" O VAL A 572 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N ALA A 574 " --> pdb=" O ALA A 487 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ILE A 489 " --> pdb=" O ALA A 574 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ASP A 571 " --> pdb=" O LYS A 606 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 632 through 634 removed outlier: 6.292A pdb=" N TYR A 632 " --> pdb=" O VAL A 653 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N LEU A 655 " --> pdb=" O TYR A 632 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N THR A 634 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 9.245A pdb=" N LYS A 657 " --> pdb=" O THR A 634 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ASP A 662 " --> pdb=" O TRP A 677 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N TRP A 677 " --> pdb=" O ASP A 662 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE A 664 " --> pdb=" O LEU A 675 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 3 through 9 removed outlier: 5.648A pdb=" N ILE B 3 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N VAL B 24 " --> pdb=" O ILE B 3 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU B 111 " --> pdb=" O ALA B 98 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ALA B 98 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N SER B 113 " --> pdb=" O GLY B 96 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 180 through 182 Processing sheet with id=AB1, first strand: chain 'B' and resid 270 through 273 removed outlier: 6.190A pdb=" N VAL B 256 " --> pdb=" O ASN B 272 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 313 through 318 removed outlier: 7.001A pdb=" N LEU B 307 " --> pdb=" O VAL B 314 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA B 316 " --> pdb=" O ARG B 305 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ARG B 305 " --> pdb=" O ALA B 316 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ARG B 318 " --> pdb=" O ASP B 303 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASP B 303 " --> pdb=" O ARG B 318 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASP B 427 " --> pdb=" O CYS B 445 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 323 through 325 Processing sheet with id=AB4, first strand: chain 'B' and resid 526 through 527 removed outlier: 7.861A pdb=" N GLY B 514 " --> pdb=" O VAL B 552 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE B 486 " --> pdb=" O ALA B 551 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N LEU B 553 " --> pdb=" O ILE B 486 " (cutoff:3.500A) removed outlier: 9.642A pdb=" N ALA B 488 " --> pdb=" O LEU B 553 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ALA B 487 " --> pdb=" O VAL B 572 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N ALA B 574 " --> pdb=" O ALA B 487 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N ILE B 489 " --> pdb=" O ALA B 574 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ASP B 571 " --> pdb=" O LYS B 606 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 632 through 634 removed outlier: 6.292A pdb=" N TYR B 632 " --> pdb=" O VAL B 653 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N LEU B 655 " --> pdb=" O TYR B 632 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N THR B 634 " --> pdb=" O LEU B 655 " (cutoff:3.500A) removed outlier: 9.245A pdb=" N LYS B 657 " --> pdb=" O THR B 634 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ASP B 662 " --> pdb=" O TRP B 677 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N TRP B 677 " --> pdb=" O ASP B 662 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE B 664 " --> pdb=" O LEU B 675 " (cutoff:3.500A) 424 hydrogen bonds defined for protein. 1128 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: 1.53 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1989 1.31 - 1.44: 2642 1.44 - 1.57: 6293 1.57 - 1.70: 112 1.70 - 1.83: 80 Bond restraints: 11116 Sorted by residual: bond pdb=" CB HIS A 645 " pdb=" CG HIS A 645 " ideal model delta sigma weight residual 1.497 1.416 0.081 1.40e-02 5.10e+03 3.35e+01 bond pdb=" CB HIS B 645 " pdb=" CG HIS B 645 " ideal model delta sigma weight residual 1.497 1.417 0.080 1.40e-02 5.10e+03 3.28e+01 bond pdb=" CB TYR B 114 " pdb=" CG TYR B 114 " ideal model delta sigma weight residual 1.512 1.395 0.117 2.20e-02 2.07e+03 2.85e+01 bond pdb=" CB TYR A 114 " pdb=" CG TYR A 114 " ideal model delta sigma weight residual 1.512 1.395 0.117 2.20e-02 2.07e+03 2.80e+01 bond pdb=" CB LEU A 183 " pdb=" CG LEU A 183 " ideal model delta sigma weight residual 1.530 1.629 -0.099 2.00e-02 2.50e+03 2.43e+01 ... (remaining 11111 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.80: 13337 2.80 - 5.61: 1524 5.61 - 8.41: 202 8.41 - 11.22: 17 11.22 - 14.02: 2 Bond angle restraints: 15082 Sorted by residual: angle pdb=" N LEU B 591 " pdb=" CA LEU B 591 " pdb=" C LEU B 591 " ideal model delta sigma weight residual 113.88 99.86 14.02 1.23e+00 6.61e-01 1.30e+02 angle pdb=" N LEU A 591 " pdb=" CA LEU A 591 " pdb=" C LEU A 591 " ideal model delta sigma weight residual 113.88 99.87 14.01 1.23e+00 6.61e-01 1.30e+02 angle pdb=" CA ASP A 662 " pdb=" CB ASP A 662 " pdb=" CG ASP A 662 " ideal model delta sigma weight residual 112.60 121.57 -8.97 1.00e+00 1.00e+00 8.04e+01 angle pdb=" CA ASP B 662 " pdb=" CB ASP B 662 " pdb=" CG ASP B 662 " ideal model delta sigma weight residual 112.60 121.51 -8.91 1.00e+00 1.00e+00 7.94e+01 angle pdb=" N THR A 52 " pdb=" CA THR A 52 " pdb=" C THR A 52 " ideal model delta sigma weight residual 114.56 104.13 10.43 1.27e+00 6.20e-01 6.75e+01 ... (remaining 15077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 6457 17.54 - 35.08: 202 35.08 - 52.62: 39 52.62 - 70.16: 14 70.16 - 87.70: 4 Dihedral angle restraints: 6716 sinusoidal: 2632 harmonic: 4084 Sorted by residual: dihedral pdb=" C TRP A 677 " pdb=" N TRP A 677 " pdb=" CA TRP A 677 " pdb=" CB TRP A 677 " ideal model delta harmonic sigma weight residual -122.60 -113.60 -9.00 0 2.50e+00 1.60e-01 1.30e+01 dihedral pdb=" N PHE B 254 " pdb=" C PHE B 254 " pdb=" CA PHE B 254 " pdb=" CB PHE B 254 " ideal model delta harmonic sigma weight residual 122.80 131.80 -9.00 0 2.50e+00 1.60e-01 1.30e+01 dihedral pdb=" C TRP B 677 " pdb=" N TRP B 677 " pdb=" CA TRP B 677 " pdb=" CB TRP B 677 " ideal model delta harmonic sigma weight residual -122.60 -113.61 -8.99 0 2.50e+00 1.60e-01 1.29e+01 ... (remaining 6713 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1197 0.097 - 0.193: 465 0.193 - 0.290: 96 0.290 - 0.387: 8 0.387 - 0.484: 2 Chirality restraints: 1768 Sorted by residual: chirality pdb=" CA PHE A 254 " pdb=" N PHE A 254 " pdb=" C PHE A 254 " pdb=" CB PHE A 254 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.85e+00 chirality pdb=" CA PHE B 254 " pdb=" N PHE B 254 " pdb=" C PHE B 254 " pdb=" CB PHE B 254 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.82e+00 chirality pdb=" CA SER A 209 " pdb=" N SER A 209 " pdb=" C SER A 209 " pdb=" CB SER A 209 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.51e+00 ... (remaining 1765 not shown) Planarity restraints: 1964 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 196 " 0.055 2.00e-02 2.50e+03 2.92e-02 1.71e+01 pdb=" CG TYR A 196 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR A 196 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR A 196 " -0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR A 196 " -0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR A 196 " -0.015 2.00e-02 2.50e+03 pdb=" CZ TYR A 196 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 196 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 196 " -0.055 2.00e-02 2.50e+03 2.91e-02 1.70e+01 pdb=" CG TYR B 196 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR B 196 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR B 196 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR B 196 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR B 196 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR B 196 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 196 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 31 " 0.047 2.00e-02 2.50e+03 2.67e-02 1.42e+01 pdb=" CG TYR A 31 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR A 31 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR A 31 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR A 31 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR A 31 " -0.019 2.00e-02 2.50e+03 pdb=" CZ TYR A 31 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 31 " 0.040 2.00e-02 2.50e+03 ... (remaining 1961 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 4442 2.90 - 3.40: 10910 3.40 - 3.90: 18562 3.90 - 4.40: 22124 4.40 - 4.90: 34208 Nonbonded interactions: 90246 Sorted by model distance: nonbonded pdb=" N LEU B 591 " pdb=" N ASP B 592 " model vdw 2.398 2.560 nonbonded pdb=" N LEU A 591 " pdb=" N ASP A 592 " model vdw 2.398 2.560 nonbonded pdb=" N ASP A 145 " pdb=" OD1 ASP A 145 " model vdw 2.425 3.120 nonbonded pdb=" N ASP B 145 " pdb=" OD1 ASP B 145 " model vdw 2.425 3.120 nonbonded pdb=" N THR B 52 " pdb=" N LEU B 53 " model vdw 2.439 2.560 ... (remaining 90241 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 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: 1.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.500 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5265 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 : 0.018 0.117 11116 Z= 0.982 Angle : 1.880 14.020 15082 Z= 1.274 Chirality : 0.101 0.484 1768 Planarity : 0.009 0.031 1964 Dihedral : 9.930 87.702 4108 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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: -1.52 (0.21), residues: 1434 helix: -1.40 (0.20), residues: 468 sheet: 0.55 (0.44), residues: 148 loop : -1.03 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 438 TYR 0.055 0.010 TYR A 196 PHE 0.015 0.006 PHE A 153 TRP 0.017 0.006 TRP A 180 HIS 0.007 0.002 HIS B 679 Details of bonding type rmsd/Z covalent geometry : bond 0.01807 / 0.98 (11116) covalent geometry : angle 1.88043 / 1.27 (15082) hydrogen bonds : bond 0.19667 / 12.93 ( 424) hydrogen bonds : angle 7.92669 / 5.60 ( 1128) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 417 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ILE cc_start: 0.8612 (mt) cc_final: 0.7663 (mt) REVERT: A 219 LYS cc_start: 0.5665 (pttm) cc_final: 0.5447 (pttt) REVERT: A 220 ASN cc_start: 0.8047 (m-40) cc_final: 0.7675 (m-40) REVERT: A 303 ASP cc_start: 0.8251 (m-30) cc_final: 0.7828 (t0) REVERT: A 336 ILE cc_start: 0.7906 (mm) cc_final: 0.7660 (mm) REVERT: A 386 ARG cc_start: 0.7797 (mmt-90) cc_final: 0.7364 (mmm-85) REVERT: A 448 ASN cc_start: 0.5545 (t0) cc_final: 0.4761 (t0) REVERT: A 508 MET cc_start: 0.6755 (mmp) cc_final: 0.6046 (mtp) REVERT: A 521 VAL cc_start: 0.9024 (t) cc_final: 0.8817 (m) REVERT: A 645 HIS cc_start: 0.7097 (t70) cc_final: 0.6788 (t70) REVERT: A 697 MET cc_start: 0.5429 (mtp) cc_final: 0.5200 (mtp) REVERT: B 21 ILE cc_start: 0.8600 (mt) cc_final: 0.7604 (mt) REVERT: B 220 ASN cc_start: 0.8141 (m-40) cc_final: 0.7685 (m-40) REVERT: B 303 ASP cc_start: 0.8182 (m-30) cc_final: 0.7754 (t0) REVERT: B 336 ILE cc_start: 0.7699 (mm) cc_final: 0.7329 (mm) REVERT: B 386 ARG cc_start: 0.7882 (mmt-90) cc_final: 0.7502 (mmm-85) REVERT: B 421 LEU cc_start: 0.8833 (mt) cc_final: 0.8589 (mt) REVERT: B 476 PHE cc_start: 0.8317 (m-80) cc_final: 0.8076 (m-80) REVERT: B 508 MET cc_start: 0.6708 (mmp) cc_final: 0.6387 (mtp) REVERT: B 521 VAL cc_start: 0.8982 (t) cc_final: 0.8615 (m) REVERT: B 645 HIS cc_start: 0.7025 (t70) cc_final: 0.6692 (t70) REVERT: B 695 ASN cc_start: 0.8509 (m-40) cc_final: 0.8307 (m110) REVERT: B 697 MET cc_start: 0.5703 (mtp) cc_final: 0.5262 (mtp) outliers start: 0 outliers final: 0 residues processed: 417 average time/residue: 0.0983 time to fit residues: 55.7493 Evaluate side-chains 245 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 HIS A 224 GLN A 304 HIS A 481 GLN A 679 HIS ** A 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 HIS B 224 GLN B 304 HIS B 679 HIS ** B 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.183650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.155905 restraints weight = 27923.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.159147 restraints weight = 19471.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.161458 restraints weight = 14764.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.162704 restraints weight = 12031.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.164099 restraints weight = 10513.127| |-----------------------------------------------------------------------------| r_work (final): 0.4323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6327 moved from start: 0.4554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11116 Z= 0.192 Angle : 0.805 9.535 15082 Z= 0.430 Chirality : 0.049 0.239 1768 Planarity : 0.005 0.072 1964 Dihedral : 6.108 34.707 1558 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 0.17 % Allowed : 3.36 % Favored : 96.47 % 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: -1.11 (0.21), residues: 1434 helix: 0.04 (0.23), residues: 472 sheet: -0.23 (0.42), residues: 166 loop : -1.34 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 305 TYR 0.014 0.002 TYR B 704 PHE 0.018 0.003 PHE B 153 TRP 0.013 0.002 TRP B 677 HIS 0.009 0.001 HIS B 645 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.19 (11116) covalent geometry : angle 0.80517 / 0.43 (15082) hydrogen bonds : bond 0.04652 / 3.08 ( 424) hydrogen bonds : angle 6.34236 / 4.42 ( 1128) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 305 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 VAL cc_start: 0.8757 (t) cc_final: 0.8253 (p) REVERT: A 336 ILE cc_start: 0.8139 (mm) cc_final: 0.7905 (mm) REVERT: A 352 MET cc_start: 0.5996 (ptp) cc_final: 0.5700 (ptp) REVERT: A 404 ILE cc_start: 0.5116 (mm) cc_final: 0.4526 (tt) REVERT: A 409 LYS cc_start: 0.7167 (mtmt) cc_final: 0.6582 (mtpt) REVERT: A 428 PHE cc_start: 0.7542 (t80) cc_final: 0.7147 (t80) REVERT: A 430 THR cc_start: 0.8799 (t) cc_final: 0.8559 (m) REVERT: A 508 MET cc_start: 0.6833 (mmp) cc_final: 0.6196 (mtt) REVERT: A 555 THR cc_start: 0.7980 (t) cc_final: 0.7666 (t) REVERT: A 577 ASN cc_start: 0.7886 (t0) cc_final: 0.7347 (p0) REVERT: A 695 ASN cc_start: 0.8917 (m-40) cc_final: 0.8647 (m110) REVERT: B 170 VAL cc_start: 0.8787 (t) cc_final: 0.8297 (p) REVERT: B 336 ILE cc_start: 0.8020 (mm) cc_final: 0.7780 (mm) REVERT: B 385 LEU cc_start: 0.7836 (mm) cc_final: 0.7104 (tp) REVERT: B 386 ARG cc_start: 0.7723 (mmt-90) cc_final: 0.6262 (mtt180) REVERT: B 404 ILE cc_start: 0.5099 (mm) cc_final: 0.4697 (tt) REVERT: B 409 LYS cc_start: 0.7083 (mtmt) cc_final: 0.6593 (mtpt) REVERT: B 448 ASN cc_start: 0.6627 (t0) cc_final: 0.6336 (t0) REVERT: B 508 MET cc_start: 0.6918 (mmp) cc_final: 0.6380 (mtt) REVERT: B 555 THR cc_start: 0.8266 (t) cc_final: 0.8062 (p) REVERT: B 570 CYS cc_start: 0.8541 (p) cc_final: 0.8316 (p) REVERT: B 577 ASN cc_start: 0.7900 (t0) cc_final: 0.7340 (p0) REVERT: B 692 ASN cc_start: 0.6734 (m-40) cc_final: 0.6263 (t0) REVERT: B 695 ASN cc_start: 0.8984 (m-40) cc_final: 0.8729 (m110) outliers start: 2 outliers final: 2 residues processed: 307 average time/residue: 0.0907 time to fit residues: 39.3639 Evaluate side-chains 203 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 201 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 5 optimal weight: 0.2980 chunk 83 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 92 optimal weight: 0.1980 chunk 137 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 143 GLN ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 GLN A 481 GLN A 679 HIS ** B 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN B 193 GLN B 679 HIS ** B 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.177183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.147885 restraints weight = 25200.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.151490 restraints weight = 16608.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.154031 restraints weight = 12130.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.155802 restraints weight = 9590.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.156841 restraints weight = 8096.923| |-----------------------------------------------------------------------------| r_work (final): 0.4210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6410 moved from start: 0.5771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11116 Z= 0.155 Angle : 0.725 6.537 15082 Z= 0.386 Chirality : 0.048 0.379 1768 Planarity : 0.005 0.078 1964 Dihedral : 5.845 42.674 1558 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 0.09 % Allowed : 3.19 % Favored : 96.72 % 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: -1.32 (0.21), residues: 1434 helix: 0.09 (0.23), residues: 480 sheet: -0.59 (0.40), residues: 170 loop : -1.59 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 305 TYR 0.022 0.002 TYR B 156 PHE 0.021 0.003 PHE A 153 TRP 0.014 0.002 TRP B 677 HIS 0.007 0.001 HIS B 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.16 (11116) covalent geometry : angle 0.72548 / 0.39 (15082) hydrogen bonds : bond 0.04199 / 2.85 ( 424) hydrogen bonds : angle 6.04673 / 4.19 ( 1128) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 271 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 ASN cc_start: 0.8234 (m-40) cc_final: 0.7474 (m-40) REVERT: A 336 ILE cc_start: 0.8047 (mm) cc_final: 0.7758 (mm) REVERT: A 352 MET cc_start: 0.6401 (ptp) cc_final: 0.6043 (ptp) REVERT: A 355 LYS cc_start: 0.7506 (tppt) cc_final: 0.6819 (ptmt) REVERT: A 385 LEU cc_start: 0.7529 (mm) cc_final: 0.7049 (tt) REVERT: A 386 ARG cc_start: 0.7848 (mmt-90) cc_final: 0.6910 (mtt180) REVERT: A 492 THR cc_start: 0.6262 (p) cc_final: 0.5967 (p) REVERT: A 508 MET cc_start: 0.7022 (mmp) cc_final: 0.6385 (mtp) REVERT: A 570 CYS cc_start: 0.8569 (p) cc_final: 0.8358 (p) REVERT: A 621 MET cc_start: 0.7123 (mmm) cc_final: 0.6626 (mmm) REVERT: A 692 ASN cc_start: 0.6492 (t0) cc_final: 0.5900 (t0) REVERT: A 697 MET cc_start: 0.7849 (mtm) cc_final: 0.7556 (mtp) REVERT: B 220 ASN cc_start: 0.8590 (m-40) cc_final: 0.7724 (m-40) REVERT: B 336 ILE cc_start: 0.8005 (mm) cc_final: 0.7777 (mm) REVERT: B 352 MET cc_start: 0.6170 (ptp) cc_final: 0.5784 (ptt) REVERT: B 355 LYS cc_start: 0.7509 (mmmt) cc_final: 0.6736 (ptpt) REVERT: B 385 LEU cc_start: 0.7678 (mm) cc_final: 0.7179 (tt) REVERT: B 386 ARG cc_start: 0.7714 (mmt-90) cc_final: 0.5650 (mtt180) REVERT: B 409 LYS cc_start: 0.7166 (mtmt) cc_final: 0.6686 (mtpt) REVERT: B 508 MET cc_start: 0.7188 (mmp) cc_final: 0.6910 (mtp) REVERT: B 570 CYS cc_start: 0.8563 (p) cc_final: 0.8323 (p) REVERT: B 577 ASN cc_start: 0.8072 (t0) cc_final: 0.7713 (p0) REVERT: B 598 LYS cc_start: 0.9021 (ttpt) cc_final: 0.8755 (ttpt) REVERT: B 618 THR cc_start: 0.8396 (m) cc_final: 0.8157 (m) REVERT: B 692 ASN cc_start: 0.6892 (m-40) cc_final: 0.6446 (t0) REVERT: B 695 ASN cc_start: 0.8979 (m-40) cc_final: 0.8749 (m110) outliers start: 1 outliers final: 0 residues processed: 271 average time/residue: 0.1007 time to fit residues: 37.6447 Evaluate side-chains 193 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 12 optimal weight: 3.9990 chunk 100 optimal weight: 0.0470 chunk 64 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 131 optimal weight: 0.7980 chunk 11 optimal weight: 0.3980 chunk 0 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 645 HIS B 177 ASN B 645 HIS ** B 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.174642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.144690 restraints weight = 24985.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.148006 restraints weight = 16627.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.150414 restraints weight = 12278.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.152046 restraints weight = 9819.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.152980 restraints weight = 8387.869| |-----------------------------------------------------------------------------| r_work (final): 0.4154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6516 moved from start: 0.6730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11116 Z= 0.138 Angle : 0.681 7.526 15082 Z= 0.361 Chirality : 0.047 0.286 1768 Planarity : 0.005 0.074 1964 Dihedral : 5.655 42.149 1558 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.88 % Favored : 91.98 % Rotamer: Outliers : 0.09 % Allowed : 2.93 % Favored : 96.98 % 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: -1.39 (0.21), residues: 1434 helix: 0.13 (0.23), residues: 478 sheet: -0.51 (0.43), residues: 148 loop : -1.70 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 414 TYR 0.019 0.001 TYR B 156 PHE 0.021 0.003 PHE B 153 TRP 0.011 0.002 TRP A 677 HIS 0.007 0.001 HIS A 645 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (11116) covalent geometry : angle 0.68071 / 0.36 (15082) hydrogen bonds : bond 0.03611 / 2.43 ( 424) hydrogen bonds : angle 5.85001 / 4.03 ( 1128) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 236 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 VAL cc_start: 0.8730 (t) cc_final: 0.8280 (p) REVERT: A 336 ILE cc_start: 0.8231 (mm) cc_final: 0.7954 (mm) REVERT: A 352 MET cc_start: 0.6490 (ptp) cc_final: 0.5812 (ptt) REVERT: A 355 LYS cc_start: 0.7580 (tppt) cc_final: 0.6921 (ptmt) REVERT: A 541 MET cc_start: 0.7845 (mmp) cc_final: 0.7631 (mmp) REVERT: A 600 VAL cc_start: 0.8342 (t) cc_final: 0.8129 (p) REVERT: A 611 LEU cc_start: 0.9473 (mm) cc_final: 0.9194 (mp) REVERT: A 692 ASN cc_start: 0.6863 (t0) cc_final: 0.6216 (t0) REVERT: A 694 GLU cc_start: 0.8689 (pm20) cc_final: 0.8077 (pm20) REVERT: A 695 ASN cc_start: 0.8788 (m110) cc_final: 0.8435 (m110) REVERT: B 53 LEU cc_start: 0.8829 (mt) cc_final: 0.8610 (mt) REVERT: B 118 GLU cc_start: 0.6968 (mp0) cc_final: 0.6746 (tt0) REVERT: B 160 PHE cc_start: 0.6967 (m-80) cc_final: 0.6471 (m-10) REVERT: B 220 ASN cc_start: 0.8483 (m-40) cc_final: 0.7831 (m-40) REVERT: B 336 ILE cc_start: 0.8072 (mm) cc_final: 0.7858 (mm) REVERT: B 352 MET cc_start: 0.5997 (ptp) cc_final: 0.5668 (ptt) REVERT: B 386 ARG cc_start: 0.7774 (mmt-90) cc_final: 0.6134 (mtt90) REVERT: B 430 THR cc_start: 0.9069 (t) cc_final: 0.8781 (m) REVERT: B 492 THR cc_start: 0.6116 (p) cc_final: 0.5915 (p) REVERT: B 692 ASN cc_start: 0.6916 (m-40) cc_final: 0.6546 (t0) REVERT: B 695 ASN cc_start: 0.8919 (m-40) cc_final: 0.8647 (m110) outliers start: 1 outliers final: 0 residues processed: 237 average time/residue: 0.0869 time to fit residues: 29.7264 Evaluate side-chains 185 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 83 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 129 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 190 GLN ** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 GLN ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 GLN B 405 HIS ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.166607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.134906 restraints weight = 25745.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.137974 restraints weight = 17373.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.140114 restraints weight = 13042.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.141719 restraints weight = 10642.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.142786 restraints weight = 9177.173| |-----------------------------------------------------------------------------| r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 moved from start: 0.7852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11116 Z= 0.202 Angle : 0.778 9.798 15082 Z= 0.414 Chirality : 0.050 0.487 1768 Planarity : 0.005 0.073 1964 Dihedral : 6.209 49.204 1558 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.97 % Favored : 89.89 % Rotamer: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % 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: -1.86 (0.21), residues: 1434 helix: -0.30 (0.23), residues: 498 sheet: -0.88 (0.40), residues: 170 loop : -2.00 (0.21), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 345 TYR 0.015 0.002 TYR A 617 PHE 0.038 0.004 PHE B 698 TRP 0.006 0.001 TRP B 180 HIS 0.009 0.002 HIS B 504 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.20 (11116) covalent geometry : angle 0.77808 / 0.41 (15082) hydrogen bonds : bond 0.04167 / 2.74 ( 424) hydrogen bonds : angle 6.00612 / 4.13 ( 1128) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ARG cc_start: 0.6139 (mmt180) cc_final: 0.5836 (mmt180) REVERT: A 53 LEU cc_start: 0.8874 (mt) cc_final: 0.8659 (mp) REVERT: A 170 VAL cc_start: 0.8869 (t) cc_final: 0.8521 (p) REVERT: A 287 MET cc_start: 0.8035 (tpp) cc_final: 0.7832 (tpp) REVERT: A 336 ILE cc_start: 0.8129 (mm) cc_final: 0.7903 (mm) REVERT: A 352 MET cc_start: 0.6310 (ptp) cc_final: 0.5956 (ptt) REVERT: A 386 ARG cc_start: 0.8682 (mmt-90) cc_final: 0.6722 (mtm110) REVERT: A 611 LEU cc_start: 0.9393 (mm) cc_final: 0.9106 (mm) REVERT: A 692 ASN cc_start: 0.7182 (t0) cc_final: 0.6567 (t0) REVERT: A 695 ASN cc_start: 0.8917 (m110) cc_final: 0.8649 (m110) REVERT: A 697 MET cc_start: 0.7805 (mtt) cc_final: 0.7575 (mtt) REVERT: B 53 LEU cc_start: 0.8787 (mt) cc_final: 0.8586 (mp) REVERT: B 220 ASN cc_start: 0.8254 (m-40) cc_final: 0.7911 (m-40) REVERT: B 336 ILE cc_start: 0.8171 (mm) cc_final: 0.7939 (mm) REVERT: B 355 LYS cc_start: 0.7640 (mmpt) cc_final: 0.7252 (ptpt) REVERT: B 609 VAL cc_start: 0.8038 (p) cc_final: 0.7727 (t) REVERT: B 677 TRP cc_start: 0.5274 (m-10) cc_final: 0.4706 (m-10) REVERT: B 692 ASN cc_start: 0.7367 (m-40) cc_final: 0.6993 (t0) REVERT: B 695 ASN cc_start: 0.8944 (m-40) cc_final: 0.8667 (m110) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.1043 time to fit residues: 33.1604 Evaluate side-chains 181 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 115 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 138 optimal weight: 9.9990 chunk 94 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 37 optimal weight: 0.0170 chunk 11 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 GLN ** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 504 HIS ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.168562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.137513 restraints weight = 25317.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.140697 restraints weight = 16942.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.142922 restraints weight = 12649.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.144431 restraints weight = 10233.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.145592 restraints weight = 8822.034| |-----------------------------------------------------------------------------| r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 0.8251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11116 Z= 0.147 Angle : 0.713 9.048 15082 Z= 0.374 Chirality : 0.048 0.247 1768 Planarity : 0.005 0.072 1964 Dihedral : 5.885 49.193 1558 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.79 % Favored : 91.07 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % 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: -1.50 (0.21), residues: 1434 helix: 0.09 (0.23), residues: 484 sheet: -0.50 (0.40), residues: 156 loop : -1.86 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 483 TYR 0.019 0.001 TYR A 617 PHE 0.019 0.002 PHE B 153 TRP 0.006 0.001 TRP B 180 HIS 0.009 0.001 HIS A 504 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (11116) covalent geometry : angle 0.71344 / 0.37 (15082) hydrogen bonds : bond 0.03768 / 2.54 ( 424) hydrogen bonds : angle 5.79622 / 3.97 ( 1128) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 VAL cc_start: 0.8784 (t) cc_final: 0.8400 (p) REVERT: A 246 VAL cc_start: 0.8759 (t) cc_final: 0.8540 (t) REVERT: A 336 ILE cc_start: 0.8273 (mm) cc_final: 0.8040 (mm) REVERT: A 352 MET cc_start: 0.6396 (ptp) cc_final: 0.6000 (ptt) REVERT: A 562 ARG cc_start: 0.8163 (tmm-80) cc_final: 0.7949 (tmm-80) REVERT: A 603 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7350 (tp30) REVERT: A 611 LEU cc_start: 0.9375 (mm) cc_final: 0.8986 (mm) REVERT: A 677 TRP cc_start: 0.5064 (m-10) cc_final: 0.4832 (m-10) REVERT: A 692 ASN cc_start: 0.7194 (t0) cc_final: 0.6536 (t0) REVERT: A 702 MET cc_start: 0.8506 (mmm) cc_final: 0.8269 (mmm) REVERT: B 170 VAL cc_start: 0.8821 (t) cc_final: 0.8430 (p) REVERT: B 220 ASN cc_start: 0.8369 (m-40) cc_final: 0.7961 (m-40) REVERT: B 336 ILE cc_start: 0.8133 (mm) cc_final: 0.7903 (mm) REVERT: B 355 LYS cc_start: 0.7607 (mmpt) cc_final: 0.7095 (ptpt) REVERT: B 603 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7712 (mm-30) REVERT: B 633 VAL cc_start: 0.8650 (t) cc_final: 0.8442 (t) REVERT: B 677 TRP cc_start: 0.5254 (m-10) cc_final: 0.4834 (m-10) REVERT: B 692 ASN cc_start: 0.7348 (m-40) cc_final: 0.6984 (t0) REVERT: B 695 ASN cc_start: 0.8824 (m-40) cc_final: 0.8597 (m110) REVERT: B 702 MET cc_start: 0.8442 (mmm) cc_final: 0.8158 (mmm) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.0848 time to fit residues: 28.4732 Evaluate side-chains 188 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 37 optimal weight: 0.0050 chunk 82 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 104 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 GLN ** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 695 ASN ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.167272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.136052 restraints weight = 25822.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.139038 restraints weight = 17661.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.141197 restraints weight = 13370.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.142712 restraints weight = 10927.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.143789 restraints weight = 9486.872| |-----------------------------------------------------------------------------| r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6821 moved from start: 0.8809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11116 Z= 0.156 Angle : 0.723 8.836 15082 Z= 0.380 Chirality : 0.050 0.425 1768 Planarity : 0.005 0.072 1964 Dihedral : 5.914 47.156 1558 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.97 % Favored : 89.89 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % 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: -1.75 (0.21), residues: 1434 helix: -0.03 (0.23), residues: 494 sheet: -0.84 (0.39), residues: 166 loop : -2.07 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 483 TYR 0.016 0.001 TYR B 156 PHE 0.018 0.003 PHE B 153 TRP 0.008 0.001 TRP B 677 HIS 0.009 0.001 HIS A 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 (11116) covalent geometry : angle 0.72293 / 0.38 (15082) hydrogen bonds : bond 0.03784 / 2.52 ( 424) hydrogen bonds : angle 5.88702 / 4.01 ( 1128) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 VAL cc_start: 0.8827 (t) cc_final: 0.8435 (p) REVERT: A 336 ILE cc_start: 0.8316 (mm) cc_final: 0.8059 (mm) REVERT: A 352 MET cc_start: 0.6157 (ptp) cc_final: 0.5932 (ptt) REVERT: A 355 LYS cc_start: 0.7638 (tppt) cc_final: 0.6890 (ptmt) REVERT: A 501 MET cc_start: 0.7135 (mmm) cc_final: 0.6859 (mmm) REVERT: A 611 LEU cc_start: 0.9368 (mm) cc_final: 0.9060 (mm) REVERT: A 692 ASN cc_start: 0.7352 (t0) cc_final: 0.6999 (t0) REVERT: B 170 VAL cc_start: 0.8823 (t) cc_final: 0.8410 (p) REVERT: B 220 ASN cc_start: 0.8117 (m-40) cc_final: 0.7895 (m-40) REVERT: B 336 ILE cc_start: 0.8123 (mm) cc_final: 0.7875 (mm) REVERT: B 355 LYS cc_start: 0.7603 (mmpt) cc_final: 0.7094 (ptpt) REVERT: B 501 MET cc_start: 0.7577 (mmp) cc_final: 0.7308 (mmp) REVERT: B 603 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7241 (mm-30) REVERT: B 621 MET cc_start: 0.6381 (mmm) cc_final: 0.5802 (mtt) REVERT: B 694 GLU cc_start: 0.8561 (pm20) cc_final: 0.8182 (pm20) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.0803 time to fit residues: 27.0019 Evaluate side-chains 189 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 89 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 140 optimal weight: 0.8980 chunk 66 optimal weight: 9.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN A 695 ASN ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 695 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.165401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.134373 restraints weight = 25707.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.137214 restraints weight = 17840.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.139241 restraints weight = 13643.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.140611 restraints weight = 11250.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.141698 restraints weight = 9842.507| |-----------------------------------------------------------------------------| r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.9340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11116 Z= 0.162 Angle : 0.737 9.374 15082 Z= 0.386 Chirality : 0.051 0.489 1768 Planarity : 0.005 0.074 1964 Dihedral : 6.135 56.207 1558 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.90 % Favored : 89.96 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % 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: -1.87 (0.21), residues: 1434 helix: -0.18 (0.23), residues: 496 sheet: -0.84 (0.38), residues: 166 loop : -2.12 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 89 TYR 0.025 0.001 TYR B 156 PHE 0.026 0.003 PHE A 153 TRP 0.005 0.001 TRP B 180 HIS 0.011 0.001 HIS B 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (11116) covalent geometry : angle 0.73654 / 0.39 (15082) hydrogen bonds : bond 0.03872 / 2.59 ( 424) hydrogen bonds : angle 5.78864 / 3.93 ( 1128) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 TYR cc_start: 0.3846 (t80) cc_final: 0.3245 (t80) REVERT: A 170 VAL cc_start: 0.8830 (t) cc_final: 0.8426 (p) REVERT: A 220 ASN cc_start: 0.8331 (m-40) cc_final: 0.7714 (t0) REVERT: A 277 GLU cc_start: 0.9020 (tm-30) cc_final: 0.8724 (tt0) REVERT: A 336 ILE cc_start: 0.8336 (mm) cc_final: 0.8061 (mm) REVERT: A 352 MET cc_start: 0.6012 (ptp) cc_final: 0.5779 (ptt) REVERT: A 355 LYS cc_start: 0.7572 (tppt) cc_final: 0.6963 (ptmt) REVERT: A 409 LYS cc_start: 0.8198 (mtmt) cc_final: 0.7714 (ptmt) REVERT: A 476 PHE cc_start: 0.8687 (m-80) cc_final: 0.8467 (m-80) REVERT: A 501 MET cc_start: 0.7406 (mmm) cc_final: 0.7056 (mmm) REVERT: A 598 LYS cc_start: 0.9083 (tmmt) cc_final: 0.8759 (tmmt) REVERT: A 603 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7438 (tp30) REVERT: A 611 LEU cc_start: 0.9293 (mm) cc_final: 0.8962 (mm) REVERT: A 692 ASN cc_start: 0.7445 (t0) cc_final: 0.7142 (t0) REVERT: A 697 MET cc_start: 0.7960 (mtp) cc_final: 0.7585 (mtt) REVERT: A 702 MET cc_start: 0.8638 (mmm) cc_final: 0.8387 (mmm) REVERT: B 156 TYR cc_start: 0.7389 (m-80) cc_final: 0.7147 (m-80) REVERT: B 170 VAL cc_start: 0.8810 (t) cc_final: 0.8268 (p) REVERT: B 220 ASN cc_start: 0.8122 (m-40) cc_final: 0.7809 (m-40) REVERT: B 336 ILE cc_start: 0.8279 (mm) cc_final: 0.8071 (mm) REVERT: B 355 LYS cc_start: 0.7770 (mmpt) cc_final: 0.7343 (ptpt) REVERT: B 386 ARG cc_start: 0.8286 (mmt-90) cc_final: 0.6409 (mtt180) REVERT: B 409 LYS cc_start: 0.8190 (mtmt) cc_final: 0.7727 (ptmt) REVERT: B 472 MET cc_start: 0.8763 (tpp) cc_final: 0.8326 (mtt) REVERT: B 541 MET cc_start: 0.6706 (mmm) cc_final: 0.6370 (mmm) REVERT: B 603 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7382 (mm-30) REVERT: B 621 MET cc_start: 0.6417 (mmm) cc_final: 0.5818 (mtt) REVERT: B 692 ASN cc_start: 0.6902 (t0) cc_final: 0.6301 (t0) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.0808 time to fit residues: 27.5288 Evaluate side-chains 187 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 70 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 132 optimal weight: 0.0570 chunk 37 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 64 optimal weight: 0.4980 chunk 72 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 57 optimal weight: 0.2980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 GLN ** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 695 ASN ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 HIS B 695 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.168537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.137826 restraints weight = 25598.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.140842 restraints weight = 17584.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.142966 restraints weight = 13324.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.144398 restraints weight = 10905.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.145551 restraints weight = 9478.746| |-----------------------------------------------------------------------------| r_work (final): 0.4070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6799 moved from start: 0.9618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11116 Z= 0.129 Angle : 0.696 8.095 15082 Z= 0.364 Chirality : 0.050 0.474 1768 Planarity : 0.005 0.071 1964 Dihedral : 5.816 54.924 1558 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.90 % Favored : 89.96 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % 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: -1.84 (0.21), residues: 1434 helix: -0.15 (0.23), residues: 500 sheet: -0.55 (0.38), residues: 172 loop : -2.20 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 483 TYR 0.024 0.001 TYR B 156 PHE 0.019 0.002 PHE B 153 TRP 0.005 0.001 TRP B 180 HIS 0.009 0.001 HIS A 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (11116) covalent geometry : angle 0.69601 / 0.36 (15082) hydrogen bonds : bond 0.03480 / 2.37 ( 424) hydrogen bonds : angle 5.63613 / 3.83 ( 1128) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 VAL cc_start: 0.8743 (t) cc_final: 0.8315 (p) REVERT: A 220 ASN cc_start: 0.8195 (m-40) cc_final: 0.7638 (t0) REVERT: A 277 GLU cc_start: 0.8875 (tm-30) cc_final: 0.8606 (tt0) REVERT: A 336 ILE cc_start: 0.8221 (mm) cc_final: 0.7937 (mm) REVERT: A 352 MET cc_start: 0.6030 (ptp) cc_final: 0.5811 (ptt) REVERT: A 355 LYS cc_start: 0.7584 (tppt) cc_final: 0.6955 (ptmt) REVERT: A 409 LYS cc_start: 0.8407 (mtmt) cc_final: 0.7932 (ptmt) REVERT: A 430 THR cc_start: 0.9051 (t) cc_final: 0.8711 (m) REVERT: A 501 MET cc_start: 0.7491 (mmm) cc_final: 0.7196 (mmm) REVERT: A 508 MET cc_start: 0.8058 (mtm) cc_final: 0.7674 (mtm) REVERT: A 603 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7362 (tp30) REVERT: A 644 GLU cc_start: 0.7339 (pm20) cc_final: 0.6407 (mm-30) REVERT: A 692 ASN cc_start: 0.7246 (t0) cc_final: 0.6563 (t0) REVERT: B 156 TYR cc_start: 0.7442 (m-80) cc_final: 0.7112 (m-80) REVERT: B 170 VAL cc_start: 0.8750 (t) cc_final: 0.8209 (p) REVERT: B 220 ASN cc_start: 0.8199 (m-40) cc_final: 0.7882 (m-40) REVERT: B 336 ILE cc_start: 0.8380 (mm) cc_final: 0.8152 (mm) REVERT: B 352 MET cc_start: 0.6383 (ptt) cc_final: 0.6053 (ptm) REVERT: B 355 LYS cc_start: 0.7578 (mmpt) cc_final: 0.7224 (ptpt) REVERT: B 386 ARG cc_start: 0.8089 (mmt-90) cc_final: 0.6033 (mtt180) REVERT: B 409 LYS cc_start: 0.7930 (mtmt) cc_final: 0.7501 (ptmt) REVERT: B 430 THR cc_start: 0.8957 (t) cc_final: 0.8667 (m) REVERT: B 472 MET cc_start: 0.8729 (tpp) cc_final: 0.8225 (mtt) REVERT: B 621 MET cc_start: 0.6485 (mmm) cc_final: 0.5900 (mtt) REVERT: B 692 ASN cc_start: 0.6563 (t0) cc_final: 0.5866 (t0) outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.0802 time to fit residues: 27.7904 Evaluate side-chains 188 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 27 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 GLN ** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 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 = 0.4318 r_free = 0.4318 target = 0.164066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.133819 restraints weight = 26678.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.136540 restraints weight = 18631.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.138455 restraints weight = 14351.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.139847 restraints weight = 11905.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.140656 restraints weight = 10400.603| |-----------------------------------------------------------------------------| r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 1.0134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 11116 Z= 0.170 Angle : 0.755 10.108 15082 Z= 0.395 Chirality : 0.051 0.484 1768 Planarity : 0.005 0.074 1964 Dihedral : 6.305 58.583 1558 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.02 % Favored : 88.84 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % 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: -1.96 (0.21), residues: 1434 helix: -0.31 (0.23), residues: 484 sheet: -0.57 (0.38), residues: 178 loop : -2.21 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 483 TYR 0.024 0.002 TYR B 617 PHE 0.028 0.002 PHE B 153 TRP 0.003 0.001 TRP B 677 HIS 0.006 0.001 HIS B 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 (11116) covalent geometry : angle 0.75511 / 0.39 (15082) hydrogen bonds : bond 0.03831 / 2.57 ( 424) hydrogen bonds : angle 5.82132 / 3.96 ( 1128) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 TYR cc_start: 0.7731 (m-80) cc_final: 0.7434 (m-80) REVERT: A 170 VAL cc_start: 0.8816 (t) cc_final: 0.8458 (p) REVERT: A 220 ASN cc_start: 0.8364 (m-40) cc_final: 0.7743 (t0) REVERT: A 277 GLU cc_start: 0.8923 (tm-30) cc_final: 0.8676 (tt0) REVERT: A 336 ILE cc_start: 0.8323 (mm) cc_final: 0.8045 (mm) REVERT: A 355 LYS cc_start: 0.7893 (tppt) cc_final: 0.7119 (ptmt) REVERT: A 409 LYS cc_start: 0.8631 (mtmt) cc_final: 0.8305 (mtmt) REVERT: A 644 GLU cc_start: 0.7622 (pm20) cc_final: 0.6164 (tp30) REVERT: A 692 ASN cc_start: 0.7343 (t0) cc_final: 0.6673 (t0) REVERT: B 156 TYR cc_start: 0.7529 (m-80) cc_final: 0.7180 (m-80) REVERT: B 170 VAL cc_start: 0.8842 (t) cc_final: 0.8362 (p) REVERT: B 220 ASN cc_start: 0.8161 (m-40) cc_final: 0.7825 (m-40) REVERT: B 336 ILE cc_start: 0.8254 (mm) cc_final: 0.8051 (mm) REVERT: B 355 LYS cc_start: 0.7877 (mmpt) cc_final: 0.7324 (ptmt) REVERT: B 409 LYS cc_start: 0.8574 (mtmt) cc_final: 0.8231 (mtmt) REVERT: B 472 MET cc_start: 0.8867 (tpp) cc_final: 0.8380 (mtt) REVERT: B 473 ASP cc_start: 0.8557 (m-30) cc_final: 0.8349 (m-30) REVERT: B 555 THR cc_start: 0.8985 (p) cc_final: 0.8765 (p) REVERT: B 603 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7471 (tp30) REVERT: B 621 MET cc_start: 0.6604 (mmm) cc_final: 0.5896 (mtt) REVERT: B 692 ASN cc_start: 0.6871 (t0) cc_final: 0.6200 (t0) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.0847 time to fit residues: 27.8815 Evaluate side-chains 185 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 5 optimal weight: 0.0370 chunk 31 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 137 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 134 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 HIS ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.163088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.132655 restraints weight = 27235.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.135282 restraints weight = 19297.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.137164 restraints weight = 15037.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.138486 restraints weight = 12510.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.139199 restraints weight = 10998.969| |-----------------------------------------------------------------------------| r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 1.0517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11116 Z= 0.177 Angle : 0.754 8.777 15082 Z= 0.398 Chirality : 0.051 0.470 1768 Planarity : 0.005 0.076 1964 Dihedral : 6.405 62.273 1558 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.88 % Favored : 88.98 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % 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: -2.21 (0.21), residues: 1434 helix: -0.55 (0.22), residues: 498 sheet: -0.91 (0.36), residues: 198 loop : -2.33 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 159 TYR 0.023 0.002 TYR B 156 PHE 0.025 0.003 PHE A 698 TRP 0.006 0.001 TRP A 677 HIS 0.008 0.002 HIS B 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 (11116) covalent geometry : angle 0.75392 / 0.40 (15082) hydrogen bonds : bond 0.03752 / 2.55 ( 424) hydrogen bonds : angle 5.94853 / 4.04 ( 1128) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1591.12 seconds wall clock time: 28 minutes 10.66 seconds (1690.66 seconds total)