Starting phenix.real_space_refine on Sat Aug 23 05:38:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8syn_40885/08_2025/8syn_40885.cif Found real_map, /net/cci-nas-00/data/ceres_data/8syn_40885/08_2025/8syn_40885.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8syn_40885/08_2025/8syn_40885.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8syn_40885/08_2025/8syn_40885.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8syn_40885/08_2025/8syn_40885.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8syn_40885/08_2025/8syn_40885.map" } resolution = 2.94 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= 0.001 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 6487 2.51 5 N 1695 2.21 5 O 1825 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10069 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 802, 6474 Classifications: {'peptide': 802} Link IDs: {'PTRANS': 31, 'TRANS': 770} Chain breaks: 3 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1463 Classifications: {'peptide': 184} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 175} Chain: "C" Number of atoms: 2132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2132 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 257} Chain breaks: 5 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 1.77, per 1000 atoms: 0.18 Number of scatterers: 10069 At special positions: 0 Unit cell: (78.6176, 108.365, 172.109, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 1825 8.00 N 1695 7.00 C 6487 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: 0.78 Conformation dependent library (CDL) restraints added in 392.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2410 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 10 sheets defined 53.5% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 12 through 21 Processing helix chain 'A' and resid 116 through 128 removed outlier: 3.805A pdb=" N LYS A 120 " --> pdb=" O PRO A 116 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY A 122 " --> pdb=" O THR A 118 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU A 123 " --> pdb=" O ASN A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 201 Processing helix chain 'A' and resid 203 through 218 removed outlier: 3.731A pdb=" N LEU A 218 " --> pdb=" O CYS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'A' and resid 226 through 254 removed outlier: 3.628A pdb=" N ASP A 236 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE A 237 " --> pdb=" O LEU A 233 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 286 Processing helix chain 'A' and resid 289 through 300 removed outlier: 3.647A pdb=" N ILE A 300 " --> pdb=" O VAL A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 307 Processing helix chain 'A' and resid 310 through 323 Proline residue: A 317 - end of helix Processing helix chain 'A' and resid 324 through 326 No H-bonds generated for 'chain 'A' and resid 324 through 326' Processing helix chain 'A' and resid 328 through 347 Processing helix chain 'A' and resid 350 through 365 removed outlier: 4.224A pdb=" N LYS A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASN A 357 " --> pdb=" O THR A 353 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE A 358 " --> pdb=" O LEU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 368 No H-bonds generated for 'chain 'A' and resid 366 through 368' Processing helix chain 'A' and resid 370 through 381 Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 391 through 403 removed outlier: 4.004A pdb=" N TRP A 397 " --> pdb=" O PRO A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 420 Processing helix chain 'A' and resid 424 through 435 removed outlier: 3.666A pdb=" N ASN A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER A 430 " --> pdb=" O LEU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 443 Processing helix chain 'A' and resid 443 through 453 removed outlier: 3.666A pdb=" N GLU A 453 " --> pdb=" O GLY A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 473 removed outlier: 3.885A pdb=" N LEU A 464 " --> pdb=" O PRO A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 480 No H-bonds generated for 'chain 'A' and resid 478 through 480' Processing helix chain 'A' and resid 481 through 494 removed outlier: 3.569A pdb=" N VAL A 492 " --> pdb=" O GLU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 517 removed outlier: 3.879A pdb=" N VAL A 508 " --> pdb=" O ASN A 504 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU A 511 " --> pdb=" O GLU A 507 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TYR A 512 " --> pdb=" O VAL A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 534 Processing helix chain 'A' and resid 537 through 541 removed outlier: 3.805A pdb=" N GLU A 540 " --> pdb=" O ARG A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 556 Processing helix chain 'A' and resid 559 through 564 removed outlier: 3.689A pdb=" N PHE A 564 " --> pdb=" O PHE A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 576 removed outlier: 4.008A pdb=" N PHE A 576 " --> pdb=" O PHE A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 596 removed outlier: 3.607A pdb=" N GLU A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 619 Processing helix chain 'A' and resid 626 through 643 removed outlier: 3.773A pdb=" N MET A 643 " --> pdb=" O GLY A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 664 Processing helix chain 'A' and resid 667 through 689 Processing helix chain 'A' and resid 694 through 712 removed outlier: 3.736A pdb=" N ALA A 699 " --> pdb=" O ARG A 695 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE A 700 " --> pdb=" O LYS A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 715 No H-bonds generated for 'chain 'A' and resid 713 through 715' Processing helix chain 'A' and resid 717 through 734 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 753 through 755 No H-bonds generated for 'chain 'A' and resid 753 through 755' Processing helix chain 'A' and resid 768 through 784 Processing helix chain 'A' and resid 795 through 808 Processing helix chain 'A' and resid 815 through 832 removed outlier: 3.587A pdb=" N ARG A 819 " --> pdb=" O ASP A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 850 Processing helix chain 'A' and resid 853 through 881 Processing helix chain 'A' and resid 883 through 901 Processing helix chain 'A' and resid 906 through 923 removed outlier: 3.633A pdb=" N HIS A 923 " --> pdb=" O LEU A 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 30 removed outlier: 3.602A pdb=" N LYS B 27 " --> pdb=" O PRO B 23 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 55 removed outlier: 3.784A pdb=" N TYR B 50 " --> pdb=" O THR B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 111 Processing helix chain 'C' and resid 166 through 171 removed outlier: 3.862A pdb=" N ALA C 171 " --> pdb=" O VAL C 167 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 26 removed outlier: 3.589A pdb=" N ARG B 180 " --> pdb=" O VAL A 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 758 through 761 Processing sheet with id=AA3, first strand: chain 'B' and resid 76 through 81 removed outlier: 6.530A pdb=" N LYS B 85 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ILE B 116 " --> pdb=" O LYS B 85 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLY B 87 " --> pdb=" O ILE B 116 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE B 134 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER B 117 " --> pdb=" O ILE B 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 5 through 9 Processing sheet with id=AA5, first strand: chain 'C' and resid 15 through 16 Processing sheet with id=AA6, first strand: chain 'C' and resid 69 through 79 removed outlier: 5.878A pdb=" N GLN C 70 " --> pdb=" O VAL C 47 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL C 47 " --> pdb=" O GLN C 70 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE C 72 " --> pdb=" O GLY C 45 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL C 39 " --> pdb=" O MET C 78 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 69 through 79 removed outlier: 5.878A pdb=" N GLN C 70 " --> pdb=" O VAL C 47 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL C 47 " --> pdb=" O GLN C 70 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE C 72 " --> pdb=" O GLY C 45 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL C 39 " --> pdb=" O MET C 78 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 155 through 159 removed outlier: 6.726A pdb=" N LEU C 177 " --> pdb=" O GLU C 200 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 226 through 239 removed outlier: 6.962A pdb=" N LEU C 213 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASN C 234 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU C 211 " --> pdb=" O ASN C 234 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLN C 236 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N VAL C 209 " --> pdb=" O GLN C 236 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ALA C 238 " --> pdb=" O ARG C 207 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ARG C 207 " --> pdb=" O ALA C 238 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 226 through 239 removed outlier: 6.962A pdb=" N LEU C 213 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASN C 234 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU C 211 " --> pdb=" O ASN C 234 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLN C 236 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N VAL C 209 " --> pdb=" O GLN C 236 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ALA C 238 " --> pdb=" O ARG C 207 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ARG C 207 " --> pdb=" O ALA C 238 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N PHE C 272 " --> pdb=" O LEU C 292 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N HIS C 284 " --> pdb=" O LEU C 280 " (cutoff:3.500A) 610 hydrogen bonds defined for protein. 1761 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: 1.46 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3228 1.34 - 1.46: 1988 1.46 - 1.58: 4977 1.58 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 10283 Sorted by residual: bond pdb=" CG1 ILE A 712 " pdb=" CD1 ILE A 712 " ideal model delta sigma weight residual 1.513 1.444 0.069 3.90e-02 6.57e+02 3.11e+00 bond pdb=" CA ILE A 712 " pdb=" CB ILE A 712 " ideal model delta sigma weight residual 1.539 1.547 -0.008 5.40e-03 3.43e+04 2.09e+00 bond pdb=" N ILE A 712 " pdb=" CA ILE A 712 " ideal model delta sigma weight residual 1.463 1.478 -0.015 1.20e-02 6.94e+03 1.55e+00 bond pdb=" C THR A 534 " pdb=" N PRO A 535 " ideal model delta sigma weight residual 1.334 1.361 -0.027 2.34e-02 1.83e+03 1.36e+00 bond pdb=" SD MET A 395 " pdb=" CE MET A 395 " ideal model delta sigma weight residual 1.791 1.762 0.029 2.50e-02 1.60e+03 1.34e+00 ... (remaining 10278 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 13658 1.95 - 3.90: 222 3.90 - 5.85: 34 5.85 - 7.80: 4 7.80 - 9.75: 2 Bond angle restraints: 13920 Sorted by residual: angle pdb=" N ILE A 712 " pdb=" CA ILE A 712 " pdb=" CB ILE A 712 " ideal model delta sigma weight residual 110.45 115.92 -5.47 7.80e-01 1.64e+00 4.91e+01 angle pdb=" C ILE A 712 " pdb=" CA ILE A 712 " pdb=" CB ILE A 712 " ideal model delta sigma weight residual 114.00 106.87 7.13 1.31e+00 5.83e-01 2.96e+01 angle pdb=" C LEU B 44 " pdb=" N CYS B 45 " pdb=" CA CYS B 45 " ideal model delta sigma weight residual 121.54 129.09 -7.55 1.91e+00 2.74e-01 1.56e+01 angle pdb=" CB LYS A 602 " pdb=" CG LYS A 602 " pdb=" CD LYS A 602 " ideal model delta sigma weight residual 111.30 103.21 8.09 2.30e+00 1.89e-01 1.24e+01 angle pdb=" CB MET A 533 " pdb=" CG MET A 533 " pdb=" SD MET A 533 " ideal model delta sigma weight residual 112.70 102.95 9.75 3.00e+00 1.11e-01 1.06e+01 ... (remaining 13915 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 5653 17.65 - 35.31: 473 35.31 - 52.96: 67 52.96 - 70.61: 8 70.61 - 88.27: 9 Dihedral angle restraints: 6210 sinusoidal: 2513 harmonic: 3697 Sorted by residual: dihedral pdb=" CA CYS A 737 " pdb=" C CYS A 737 " pdb=" N LEU A 738 " pdb=" CA LEU A 738 " ideal model delta harmonic sigma weight residual -180.00 -161.24 -18.76 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA GLY C 148 " pdb=" C GLY C 148 " pdb=" N LYS C 149 " pdb=" CA LYS C 149 " ideal model delta harmonic sigma weight residual 180.00 161.28 18.72 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA PRO A 535 " pdb=" C PRO A 535 " pdb=" N ASP A 536 " pdb=" CA ASP A 536 " ideal model delta harmonic sigma weight residual -180.00 -162.34 -17.66 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 6207 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1131 0.040 - 0.080: 318 0.080 - 0.120: 130 0.120 - 0.160: 23 0.160 - 0.199: 1 Chirality restraints: 1603 Sorted by residual: chirality pdb=" CB ILE A 718 " pdb=" CA ILE A 718 " pdb=" CG1 ILE A 718 " pdb=" CG2 ILE A 718 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.95e-01 chirality pdb=" CA MET A 533 " pdb=" N MET A 533 " pdb=" C MET A 533 " pdb=" CB MET A 533 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.82e-01 chirality pdb=" CA PRO A 535 " pdb=" N PRO A 535 " pdb=" C PRO A 535 " pdb=" CB PRO A 535 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.75e-01 ... (remaining 1600 not shown) Planarity restraints: 1761 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 384 " -0.055 5.00e-02 4.00e+02 8.35e-02 1.11e+01 pdb=" N PRO A 385 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO A 385 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 385 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 821 " -0.019 2.00e-02 2.50e+03 1.65e-02 5.45e+00 pdb=" CG TYR A 821 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR A 821 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A 821 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 821 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 821 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR A 821 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 821 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 534 " -0.032 5.00e-02 4.00e+02 4.83e-02 3.74e+00 pdb=" N PRO A 535 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 535 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 535 " -0.027 5.00e-02 4.00e+02 ... (remaining 1758 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 453 2.73 - 3.27: 10483 3.27 - 3.81: 16677 3.81 - 4.36: 19664 4.36 - 4.90: 33992 Nonbonded interactions: 81269 Sorted by model distance: nonbonded pdb=" NZ LYS B 25 " pdb=" O ASP B 174 " model vdw 2.182 3.120 nonbonded pdb=" OH TYR A 387 " pdb=" OH TYR A 391 " model vdw 2.211 3.040 nonbonded pdb=" OE2 GLU A 297 " pdb=" NH2 ARG A 318 " model vdw 2.215 3.120 nonbonded pdb=" O PRO A 34 " pdb=" NZ LYS B 34 " model vdw 2.217 3.120 nonbonded pdb=" O PHE A 656 " pdb=" OG SER A 660 " model vdw 2.232 3.040 ... (remaining 81264 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.770 Find NCS groups from input model: 0.040 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:5.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 10283 Z= 0.167 Angle : 0.625 9.753 13920 Z= 0.341 Chirality : 0.044 0.199 1603 Planarity : 0.005 0.083 1761 Dihedral : 13.189 88.268 3800 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: 0.88 (0.25), residues: 1237 helix: 1.23 (0.21), residues: 597 sheet: 0.19 (0.38), residues: 197 loop : 0.04 (0.32), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 318 TYR 0.041 0.002 TYR A 821 PHE 0.024 0.002 PHE C 93 TRP 0.011 0.001 TRP A 490 HIS 0.014 0.001 HIS A 596 Details of bonding type rmsd covalent geometry : bond 0.00387 (10283) covalent geometry : angle 0.62483 (13920) hydrogen bonds : bond 0.13598 ( 575) hydrogen bonds : angle 6.51715 ( 1761) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 LYS cc_start: 0.7396 (tttt) cc_final: 0.7129 (tttp) REVERT: A 344 MET cc_start: 0.8505 (mmt) cc_final: 0.8076 (mpp) REVERT: A 366 LYS cc_start: 0.7729 (tptp) cc_final: 0.7400 (tppt) REVERT: A 488 GLU cc_start: 0.7811 (tp30) cc_final: 0.7489 (mm-30) REVERT: A 514 CYS cc_start: 0.7977 (m) cc_final: 0.7600 (m) REVERT: A 584 GLU cc_start: 0.6888 (tm-30) cc_final: 0.6471 (tm-30) REVERT: A 595 LYS cc_start: 0.8420 (tmmt) cc_final: 0.8197 (tmmm) REVERT: A 599 GLU cc_start: 0.7619 (pm20) cc_final: 0.7386 (mp0) REVERT: A 630 LYS cc_start: 0.7670 (mttp) cc_final: 0.7330 (mtmm) REVERT: A 659 GLU cc_start: 0.6575 (pp20) cc_final: 0.6101 (tm-30) REVERT: A 868 MET cc_start: 0.5468 (mtm) cc_final: 0.4971 (mtm) REVERT: C 14 LYS cc_start: 0.8518 (mtmt) cc_final: 0.8299 (mtmt) REVERT: C 44 GLU cc_start: 0.8046 (tt0) cc_final: 0.7820 (tt0) REVERT: C 175 LYS cc_start: 0.8205 (mppt) cc_final: 0.7831 (mppt) REVERT: C 176 PHE cc_start: 0.7972 (p90) cc_final: 0.7755 (p90) REVERT: C 231 GLU cc_start: 0.7546 (pt0) cc_final: 0.7304 (pt0) REVERT: C 269 LYS cc_start: 0.8207 (mtmm) cc_final: 0.7895 (mtmm) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.4640 time to fit residues: 131.7280 Evaluate side-chains 238 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.0570 chunk 123 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 727 HIS A 778 ASN C 115 ASN C 117 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.175084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.147454 restraints weight = 15727.278| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 2.44 r_work: 0.3728 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 10283 Z= 0.170 Angle : 0.620 7.906 13920 Z= 0.317 Chirality : 0.044 0.148 1603 Planarity : 0.005 0.062 1761 Dihedral : 4.307 19.369 1338 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.04 % Allowed : 10.09 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: 1.22 (0.25), residues: 1237 helix: 1.54 (0.21), residues: 622 sheet: 0.40 (0.39), residues: 197 loop : 0.04 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 686 TYR 0.027 0.002 TYR A 821 PHE 0.023 0.002 PHE A 796 TRP 0.015 0.002 TRP A 810 HIS 0.008 0.001 HIS A 596 Details of bonding type rmsd covalent geometry : bond 0.00403 (10283) covalent geometry : angle 0.62027 (13920) hydrogen bonds : bond 0.04374 ( 575) hydrogen bonds : angle 4.93991 ( 1761) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 247 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 ASP cc_start: 0.7741 (t0) cc_final: 0.7495 (t0) REVERT: A 344 MET cc_start: 0.8710 (mmt) cc_final: 0.8270 (mpp) REVERT: A 366 LYS cc_start: 0.7854 (tptp) cc_final: 0.7558 (tppt) REVERT: A 419 LYS cc_start: 0.8154 (ttpt) cc_final: 0.7904 (ttmt) REVERT: A 488 GLU cc_start: 0.7752 (tp30) cc_final: 0.7475 (mm-30) REVERT: A 514 CYS cc_start: 0.7845 (m) cc_final: 0.7484 (m) REVERT: A 584 GLU cc_start: 0.7199 (tm-30) cc_final: 0.6740 (tm-30) REVERT: A 595 LYS cc_start: 0.8759 (tmmt) cc_final: 0.8239 (tmmm) REVERT: A 596 HIS cc_start: 0.8323 (m170) cc_final: 0.7664 (m-70) REVERT: A 630 LYS cc_start: 0.7916 (mttp) cc_final: 0.7708 (mtmm) REVERT: A 652 GLN cc_start: 0.7109 (OUTLIER) cc_final: 0.6768 (tp-100) REVERT: A 659 GLU cc_start: 0.6695 (pp20) cc_final: 0.6221 (tm-30) REVERT: A 661 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7903 (ttm110) REVERT: A 724 LEU cc_start: 0.7949 (mt) cc_final: 0.7747 (mt) REVERT: A 868 MET cc_start: 0.7427 (mtm) cc_final: 0.6299 (mtm) REVERT: B 86 ILE cc_start: 0.6020 (tp) cc_final: 0.5681 (pp) REVERT: B 176 VAL cc_start: 0.8173 (OUTLIER) cc_final: 0.7933 (m) REVERT: C 44 GLU cc_start: 0.8195 (tt0) cc_final: 0.7969 (tt0) REVERT: C 175 LYS cc_start: 0.8125 (mppt) cc_final: 0.7748 (mppt) REVERT: C 176 PHE cc_start: 0.8041 (p90) cc_final: 0.7761 (p90) REVERT: C 269 LYS cc_start: 0.8237 (mtmm) cc_final: 0.7936 (mtmm) REVERT: C 290 PHE cc_start: 0.8353 (m-80) cc_final: 0.8126 (m-80) outliers start: 23 outliers final: 11 residues processed: 255 average time/residue: 0.4522 time to fit residues: 124.8313 Evaluate side-chains 241 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 227 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 652 GLN Chi-restraints excluded: chain A residue 661 ARG Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 277 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 122 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 111 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 112 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 75 optimal weight: 30.0000 chunk 93 optimal weight: 0.9980 chunk 34 optimal weight: 0.0980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 ASN A 727 HIS B 170 GLN C 115 ASN C 234 ASN C 289 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.174716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.147061 restraints weight = 15738.446| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 2.42 r_work: 0.3720 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10283 Z= 0.186 Angle : 0.600 8.310 13920 Z= 0.307 Chirality : 0.044 0.153 1603 Planarity : 0.004 0.053 1761 Dihedral : 4.305 19.046 1338 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.57 % Allowed : 13.27 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: 1.33 (0.25), residues: 1237 helix: 1.65 (0.21), residues: 625 sheet: 0.42 (0.39), residues: 197 loop : 0.06 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 819 TYR 0.021 0.002 TYR A 821 PHE 0.037 0.002 PHE A 796 TRP 0.013 0.002 TRP A 810 HIS 0.007 0.001 HIS A 596 Details of bonding type rmsd covalent geometry : bond 0.00442 (10283) covalent geometry : angle 0.59967 (13920) hydrogen bonds : bond 0.04221 ( 575) hydrogen bonds : angle 4.74959 ( 1761) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 240 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 ASN cc_start: 0.8054 (OUTLIER) cc_final: 0.7714 (m-40) REVERT: A 395 MET cc_start: 0.8119 (mtt) cc_final: 0.7912 (mtp) REVERT: A 419 LYS cc_start: 0.8172 (ttpt) cc_final: 0.7886 (ttmp) REVERT: A 488 GLU cc_start: 0.7761 (tp30) cc_final: 0.7514 (mm-30) REVERT: A 574 ASP cc_start: 0.7547 (OUTLIER) cc_final: 0.7324 (t0) REVERT: A 584 GLU cc_start: 0.7064 (tm-30) cc_final: 0.6614 (tm-30) REVERT: A 590 MET cc_start: 0.8423 (mmm) cc_final: 0.8074 (tpt) REVERT: A 595 LYS cc_start: 0.8767 (tmmt) cc_final: 0.8246 (tmmm) REVERT: A 630 LYS cc_start: 0.7986 (mttp) cc_final: 0.7733 (mtmm) REVERT: A 659 GLU cc_start: 0.6749 (pp20) cc_final: 0.6278 (tm-30) REVERT: A 661 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7822 (ttm110) REVERT: A 868 MET cc_start: 0.7340 (mtm) cc_final: 0.6224 (mtm) REVERT: B 122 LYS cc_start: 0.8091 (tmmt) cc_final: 0.7690 (tmmt) REVERT: B 131 LYS cc_start: 0.7666 (mmmt) cc_final: 0.7427 (mmmm) REVERT: C 13 ASN cc_start: 0.8403 (p0) cc_final: 0.8167 (p0) REVERT: C 14 LYS cc_start: 0.8600 (mtmt) cc_final: 0.8340 (mtmt) REVERT: C 44 GLU cc_start: 0.8234 (tt0) cc_final: 0.8000 (tt0) REVERT: C 95 PHE cc_start: 0.8255 (m-80) cc_final: 0.7995 (m-80) REVERT: C 175 LYS cc_start: 0.8107 (mppt) cc_final: 0.7722 (mppt) REVERT: C 176 PHE cc_start: 0.8162 (p90) cc_final: 0.7857 (p90) REVERT: C 269 LYS cc_start: 0.8245 (mtmm) cc_final: 0.7951 (mtmm) REVERT: C 290 PHE cc_start: 0.8394 (m-80) cc_final: 0.8168 (m-80) outliers start: 29 outliers final: 13 residues processed: 250 average time/residue: 0.4577 time to fit residues: 123.5017 Evaluate side-chains 248 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 232 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 375 ASN Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 661 ARG Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 289 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 88 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 44 optimal weight: 0.0870 chunk 80 optimal weight: 0.4980 chunk 77 optimal weight: 10.0000 chunk 75 optimal weight: 50.0000 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 727 HIS C 115 ASN C 289 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.175245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.147598 restraints weight = 15823.047| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 2.45 r_work: 0.3723 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 10283 Z= 0.159 Angle : 0.611 14.598 13920 Z= 0.307 Chirality : 0.044 0.177 1603 Planarity : 0.004 0.051 1761 Dihedral : 4.243 19.294 1338 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.65 % Allowed : 16.11 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: 1.44 (0.25), residues: 1237 helix: 1.76 (0.21), residues: 625 sheet: 0.40 (0.39), residues: 199 loop : 0.11 (0.33), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 819 TYR 0.030 0.002 TYR B 73 PHE 0.026 0.002 PHE A 796 TRP 0.013 0.001 TRP A 810 HIS 0.007 0.001 HIS A 596 Details of bonding type rmsd covalent geometry : bond 0.00378 (10283) covalent geometry : angle 0.61122 (13920) hydrogen bonds : bond 0.03973 ( 575) hydrogen bonds : angle 4.62997 ( 1761) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 242 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 ASP cc_start: 0.7829 (OUTLIER) cc_final: 0.7366 (t0) REVERT: A 416 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7114 (mp0) REVERT: A 419 LYS cc_start: 0.8228 (ttpt) cc_final: 0.7933 (ttmt) REVERT: A 488 GLU cc_start: 0.7825 (tp30) cc_final: 0.7561 (mm-30) REVERT: A 567 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7533 (mp0) REVERT: A 574 ASP cc_start: 0.7572 (OUTLIER) cc_final: 0.7329 (t0) REVERT: A 584 GLU cc_start: 0.7118 (tm-30) cc_final: 0.6648 (tm-30) REVERT: A 595 LYS cc_start: 0.8805 (tmmt) cc_final: 0.8598 (tmmm) REVERT: A 630 LYS cc_start: 0.7976 (mttp) cc_final: 0.7680 (mtmm) REVERT: A 659 GLU cc_start: 0.6888 (pp20) cc_final: 0.6367 (tm-30) REVERT: A 800 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7579 (mp0) REVERT: A 819 ARG cc_start: 0.7478 (mpp80) cc_final: 0.7041 (mpp80) REVERT: A 868 MET cc_start: 0.7358 (mtm) cc_final: 0.6243 (mtm) REVERT: B 29 LEU cc_start: 0.7829 (mm) cc_final: 0.7615 (mp) REVERT: B 122 LYS cc_start: 0.8134 (tmmt) cc_final: 0.7671 (tmmt) REVERT: B 131 LYS cc_start: 0.7780 (mmmt) cc_final: 0.7577 (mmmm) REVERT: C 14 LYS cc_start: 0.8645 (mtmt) cc_final: 0.8374 (mtmt) REVERT: C 43 MET cc_start: 0.8043 (tmm) cc_final: 0.7828 (ttm) REVERT: C 44 GLU cc_start: 0.8237 (tt0) cc_final: 0.8030 (tt0) REVERT: C 95 PHE cc_start: 0.8298 (m-80) cc_final: 0.7931 (m-80) REVERT: C 175 LYS cc_start: 0.8123 (mppt) cc_final: 0.7722 (mppt) REVERT: C 176 PHE cc_start: 0.8201 (p90) cc_final: 0.7955 (p90) REVERT: C 269 LYS cc_start: 0.8210 (mtmm) cc_final: 0.7913 (mtmm) REVERT: C 290 PHE cc_start: 0.8384 (m-80) cc_final: 0.8153 (m-80) outliers start: 30 outliers final: 14 residues processed: 250 average time/residue: 0.4980 time to fit residues: 134.1280 Evaluate side-chains 251 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 234 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 277 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 80 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 72 optimal weight: 50.0000 chunk 99 optimal weight: 0.9990 chunk 97 optimal weight: 0.4980 chunk 93 optimal weight: 1.9990 chunk 76 optimal weight: 30.0000 chunk 45 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN A 727 HIS A 911 GLN C 115 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.173305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.145413 restraints weight = 15918.608| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 2.45 r_work: 0.3706 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 10283 Z= 0.211 Angle : 0.623 10.738 13920 Z= 0.315 Chirality : 0.045 0.194 1603 Planarity : 0.004 0.047 1761 Dihedral : 4.305 18.588 1338 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.01 % Allowed : 17.26 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: 1.32 (0.25), residues: 1237 helix: 1.70 (0.21), residues: 623 sheet: 0.30 (0.38), residues: 199 loop : 0.03 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 121 TYR 0.025 0.002 TYR B 73 PHE 0.022 0.002 PHE A 775 TRP 0.008 0.002 TRP A 490 HIS 0.007 0.001 HIS A 596 Details of bonding type rmsd covalent geometry : bond 0.00500 (10283) covalent geometry : angle 0.62349 (13920) hydrogen bonds : bond 0.04189 ( 575) hydrogen bonds : angle 4.68029 ( 1761) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 239 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 ASP cc_start: 0.7879 (OUTLIER) cc_final: 0.7415 (t0) REVERT: A 239 ASP cc_start: 0.7570 (OUTLIER) cc_final: 0.7353 (m-30) REVERT: A 416 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7223 (mp0) REVERT: A 419 LYS cc_start: 0.8196 (ttpt) cc_final: 0.7937 (ttmt) REVERT: A 488 GLU cc_start: 0.7877 (tp30) cc_final: 0.7590 (mm-30) REVERT: A 567 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7544 (mp0) REVERT: A 574 ASP cc_start: 0.7593 (t70) cc_final: 0.7348 (t0) REVERT: A 584 GLU cc_start: 0.7125 (tm-30) cc_final: 0.6612 (tm-30) REVERT: A 595 LYS cc_start: 0.8795 (tmmt) cc_final: 0.8348 (tttm) REVERT: A 630 LYS cc_start: 0.8086 (mttp) cc_final: 0.7730 (mtmm) REVERT: A 659 GLU cc_start: 0.6974 (pp20) cc_final: 0.6530 (tm-30) REVERT: A 666 ASN cc_start: 0.7510 (t0) cc_final: 0.7225 (t0) REVERT: A 800 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7558 (mp0) REVERT: A 819 ARG cc_start: 0.7528 (mpp80) cc_final: 0.6994 (mpp80) REVERT: A 868 MET cc_start: 0.7371 (mtm) cc_final: 0.6262 (mtm) REVERT: B 29 LEU cc_start: 0.7872 (mm) cc_final: 0.7602 (mp) REVERT: B 122 LYS cc_start: 0.8140 (tmmt) cc_final: 0.7685 (tmmt) REVERT: B 131 LYS cc_start: 0.7651 (mmmt) cc_final: 0.7427 (mmmm) REVERT: B 133 TYR cc_start: 0.7666 (m-80) cc_final: 0.7451 (m-80) REVERT: C 14 LYS cc_start: 0.8630 (mtmt) cc_final: 0.8378 (mtmt) REVERT: C 44 GLU cc_start: 0.8234 (tt0) cc_final: 0.8029 (tt0) REVERT: C 95 PHE cc_start: 0.8289 (m-80) cc_final: 0.7931 (m-80) REVERT: C 175 LYS cc_start: 0.8117 (mppt) cc_final: 0.7834 (mppt) REVERT: C 176 PHE cc_start: 0.8289 (p90) cc_final: 0.7881 (p90) REVERT: C 203 GLU cc_start: 0.7821 (tt0) cc_final: 0.7155 (tt0) REVERT: C 269 LYS cc_start: 0.8211 (mtmm) cc_final: 0.7932 (mtmm) REVERT: C 290 PHE cc_start: 0.8353 (m-80) cc_final: 0.8139 (m-80) outliers start: 34 outliers final: 18 residues processed: 253 average time/residue: 0.5024 time to fit residues: 136.8899 Evaluate side-chains 258 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 237 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 652 GLN Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 217 GLU Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 289 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 96 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 48 optimal weight: 0.0040 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 727 HIS C 115 ASN C 289 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.174310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.146524 restraints weight = 15953.119| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 2.48 r_work: 0.3703 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 10283 Z= 0.197 Angle : 0.629 10.048 13920 Z= 0.317 Chirality : 0.045 0.159 1603 Planarity : 0.004 0.045 1761 Dihedral : 4.323 20.843 1338 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.57 % Allowed : 18.41 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: 1.29 (0.25), residues: 1237 helix: 1.67 (0.21), residues: 624 sheet: 0.28 (0.38), residues: 199 loop : 0.02 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 121 TYR 0.024 0.002 TYR B 73 PHE 0.023 0.002 PHE B 132 TRP 0.009 0.001 TRP A 490 HIS 0.006 0.001 HIS A 596 Details of bonding type rmsd covalent geometry : bond 0.00471 (10283) covalent geometry : angle 0.62938 (13920) hydrogen bonds : bond 0.04132 ( 575) hydrogen bonds : angle 4.68932 ( 1761) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 239 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7327 (mp0) REVERT: A 416 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7290 (mp0) REVERT: A 419 LYS cc_start: 0.8211 (ttpt) cc_final: 0.7945 (ttmt) REVERT: A 488 GLU cc_start: 0.7897 (tp30) cc_final: 0.7614 (mm-30) REVERT: A 567 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7594 (mm-30) REVERT: A 574 ASP cc_start: 0.7583 (t70) cc_final: 0.7333 (t0) REVERT: A 584 GLU cc_start: 0.7185 (tm-30) cc_final: 0.6677 (tm-30) REVERT: A 590 MET cc_start: 0.8399 (mmm) cc_final: 0.7995 (tpt) REVERT: A 595 LYS cc_start: 0.8777 (tmmt) cc_final: 0.8319 (tttm) REVERT: A 630 LYS cc_start: 0.8148 (mttp) cc_final: 0.7878 (mtmm) REVERT: A 659 GLU cc_start: 0.7228 (pp20) cc_final: 0.6650 (tm-30) REVERT: A 661 ARG cc_start: 0.8370 (tmm-80) cc_final: 0.7966 (ttt-90) REVERT: A 666 ASN cc_start: 0.7522 (t0) cc_final: 0.7202 (t0) REVERT: A 771 PHE cc_start: 0.8820 (m-80) cc_final: 0.8534 (m-80) REVERT: A 819 ARG cc_start: 0.7630 (mpp80) cc_final: 0.7184 (mpp80) REVERT: A 868 MET cc_start: 0.7374 (mtm) cc_final: 0.6268 (mtm) REVERT: B 29 LEU cc_start: 0.7877 (mm) cc_final: 0.7576 (mp) REVERT: B 122 LYS cc_start: 0.8140 (tmmt) cc_final: 0.7699 (tmmt) REVERT: B 133 TYR cc_start: 0.7711 (m-80) cc_final: 0.7455 (m-80) REVERT: C 14 LYS cc_start: 0.8621 (mtmt) cc_final: 0.8355 (mtmt) REVERT: C 41 LEU cc_start: 0.8162 (tp) cc_final: 0.7956 (tt) REVERT: C 43 MET cc_start: 0.8053 (tmm) cc_final: 0.7829 (ttm) REVERT: C 95 PHE cc_start: 0.8272 (m-80) cc_final: 0.7778 (m-80) REVERT: C 176 PHE cc_start: 0.8302 (p90) cc_final: 0.7973 (p90) REVERT: C 269 LYS cc_start: 0.8226 (mtmm) cc_final: 0.7948 (mtmm) REVERT: C 285 LEU cc_start: 0.8727 (tp) cc_final: 0.8520 (tt) outliers start: 29 outliers final: 16 residues processed: 253 average time/residue: 0.5035 time to fit residues: 137.3287 Evaluate side-chains 253 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 236 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 532 HIS Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 652 GLN Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 217 GLU Chi-restraints excluded: chain C residue 277 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 117 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 35 optimal weight: 0.0870 chunk 46 optimal weight: 0.5980 chunk 104 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 66 optimal weight: 0.0870 chunk 71 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN A 516 HIS A 727 HIS C 115 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.175124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.147330 restraints weight = 15823.761| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 2.48 r_work: 0.3721 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10283 Z= 0.153 Angle : 0.635 15.450 13920 Z= 0.313 Chirality : 0.044 0.174 1603 Planarity : 0.004 0.044 1761 Dihedral : 4.264 22.979 1338 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.57 % Allowed : 19.65 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: 1.33 (0.25), residues: 1237 helix: 1.70 (0.21), residues: 627 sheet: 0.36 (0.39), residues: 199 loop : -0.01 (0.32), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 121 TYR 0.023 0.002 TYR B 143 PHE 0.024 0.002 PHE A 745 TRP 0.008 0.001 TRP A 490 HIS 0.005 0.001 HIS A 596 Details of bonding type rmsd covalent geometry : bond 0.00366 (10283) covalent geometry : angle 0.63463 (13920) hydrogen bonds : bond 0.03899 ( 575) hydrogen bonds : angle 4.62023 ( 1761) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 241 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 SER cc_start: 0.8051 (t) cc_final: 0.7753 (t) REVERT: A 416 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7268 (mp0) REVERT: A 419 LYS cc_start: 0.8198 (ttpt) cc_final: 0.7936 (ttmt) REVERT: A 488 GLU cc_start: 0.7885 (tp30) cc_final: 0.7622 (mm-30) REVERT: A 567 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7548 (mm-30) REVERT: A 574 ASP cc_start: 0.7573 (t70) cc_final: 0.7317 (t0) REVERT: A 584 GLU cc_start: 0.7159 (tm-30) cc_final: 0.6605 (tm-30) REVERT: A 590 MET cc_start: 0.8375 (mmm) cc_final: 0.7977 (tpt) REVERT: A 595 LYS cc_start: 0.8720 (tmmt) cc_final: 0.8275 (tttm) REVERT: A 630 LYS cc_start: 0.8103 (mttp) cc_final: 0.7826 (mtmm) REVERT: A 659 GLU cc_start: 0.7289 (pp20) cc_final: 0.6865 (tm-30) REVERT: A 661 ARG cc_start: 0.8298 (tmm-80) cc_final: 0.7834 (ttt-90) REVERT: A 666 ASN cc_start: 0.7458 (t0) cc_final: 0.7132 (t0) REVERT: A 758 MET cc_start: 0.6287 (mmm) cc_final: 0.6083 (mmm) REVERT: A 819 ARG cc_start: 0.7700 (mpp80) cc_final: 0.7310 (mpp80) REVERT: A 868 MET cc_start: 0.7364 (mtm) cc_final: 0.6261 (mtm) REVERT: B 29 LEU cc_start: 0.7875 (mm) cc_final: 0.7535 (mp) REVERT: B 122 LYS cc_start: 0.8097 (tmmt) cc_final: 0.7691 (tmmt) REVERT: B 133 TYR cc_start: 0.7728 (m-80) cc_final: 0.7513 (m-80) REVERT: C 14 LYS cc_start: 0.8546 (mtmt) cc_final: 0.8281 (mtmt) REVERT: C 95 PHE cc_start: 0.8228 (m-80) cc_final: 0.7681 (m-80) REVERT: C 176 PHE cc_start: 0.8285 (p90) cc_final: 0.7916 (p90) REVERT: C 269 LYS cc_start: 0.8180 (mtmm) cc_final: 0.7907 (mtmm) REVERT: C 285 LEU cc_start: 0.8706 (tp) cc_final: 0.8499 (tt) outliers start: 29 outliers final: 20 residues processed: 252 average time/residue: 0.4894 time to fit residues: 132.8382 Evaluate side-chains 253 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 233 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 532 HIS Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 652 GLN Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 725 TYR Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 217 GLU Chi-restraints excluded: chain C residue 277 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 73 optimal weight: 10.0000 chunk 67 optimal weight: 0.9980 chunk 66 optimal weight: 0.0980 chunk 54 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 23 optimal weight: 0.1980 chunk 57 optimal weight: 4.9990 chunk 84 optimal weight: 0.0770 chunk 27 optimal weight: 0.0970 chunk 2 optimal weight: 0.4980 overall best weight: 0.1936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN A 471 ASN A 516 HIS A 727 HIS C 115 ASN C 233 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.177579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.150295 restraints weight = 15865.791| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 2.47 r_work: 0.3755 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 10283 Z= 0.126 Angle : 0.634 13.655 13920 Z= 0.314 Chirality : 0.043 0.175 1603 Planarity : 0.004 0.050 1761 Dihedral : 4.144 19.744 1338 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.12 % Allowed : 21.15 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: 1.41 (0.25), residues: 1237 helix: 1.78 (0.21), residues: 626 sheet: 0.45 (0.39), residues: 194 loop : -0.00 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 121 TYR 0.019 0.001 TYR B 73 PHE 0.020 0.001 PHE A 775 TRP 0.010 0.001 TRP A 490 HIS 0.005 0.001 HIS A 462 Details of bonding type rmsd covalent geometry : bond 0.00301 (10283) covalent geometry : angle 0.63360 (13920) hydrogen bonds : bond 0.03627 ( 575) hydrogen bonds : angle 4.52187 ( 1761) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 246 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: A 201 SER cc_start: 0.7932 (t) cc_final: 0.7633 (t) REVERT: A 248 ARG cc_start: 0.7280 (tpt90) cc_final: 0.6991 (tpt90) REVERT: A 252 MET cc_start: 0.8029 (mtt) cc_final: 0.7335 (mtt) REVERT: A 416 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7229 (mp0) REVERT: A 419 LYS cc_start: 0.8193 (ttpt) cc_final: 0.7925 (ttmt) REVERT: A 488 GLU cc_start: 0.7862 (tp30) cc_final: 0.7595 (mm-30) REVERT: A 574 ASP cc_start: 0.7569 (OUTLIER) cc_final: 0.7319 (t0) REVERT: A 584 GLU cc_start: 0.7096 (tm-30) cc_final: 0.6539 (tm-30) REVERT: A 590 MET cc_start: 0.8294 (mmm) cc_final: 0.7991 (tpt) REVERT: A 591 ASP cc_start: 0.7556 (t70) cc_final: 0.7270 (t0) REVERT: A 595 LYS cc_start: 0.8679 (tmmt) cc_final: 0.8251 (tttm) REVERT: A 630 LYS cc_start: 0.7996 (mttp) cc_final: 0.7675 (mtmm) REVERT: A 661 ARG cc_start: 0.8300 (tmm-80) cc_final: 0.7826 (ttt-90) REVERT: A 666 ASN cc_start: 0.7227 (t0) cc_final: 0.6919 (t0) REVERT: A 771 PHE cc_start: 0.8734 (m-80) cc_final: 0.8306 (m-80) REVERT: A 819 ARG cc_start: 0.7667 (mpp80) cc_final: 0.7248 (mpp80) REVERT: A 868 MET cc_start: 0.7366 (mtm) cc_final: 0.6258 (mtm) REVERT: B 29 LEU cc_start: 0.7851 (mm) cc_final: 0.7516 (mp) REVERT: B 88 LEU cc_start: 0.7204 (OUTLIER) cc_final: 0.6926 (mp) REVERT: B 122 LYS cc_start: 0.8059 (tmmt) cc_final: 0.7666 (tmmt) REVERT: C 14 LYS cc_start: 0.8563 (mtmt) cc_final: 0.8344 (mtmt) REVERT: C 42 THR cc_start: 0.8312 (m) cc_final: 0.8043 (p) REVERT: C 67 LYS cc_start: 0.7789 (mtmm) cc_final: 0.7551 (mtmm) REVERT: C 95 PHE cc_start: 0.8018 (m-80) cc_final: 0.7616 (m-80) REVERT: C 176 PHE cc_start: 0.8225 (p90) cc_final: 0.7969 (p90) REVERT: C 269 LYS cc_start: 0.8145 (mtmm) cc_final: 0.7872 (mtmm) REVERT: C 285 LEU cc_start: 0.8700 (tp) cc_final: 0.8452 (tt) outliers start: 24 outliers final: 15 residues processed: 255 average time/residue: 0.4437 time to fit residues: 122.4577 Evaluate side-chains 257 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 240 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 532 HIS Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 652 GLN Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 725 TYR Chi-restraints excluded: chain A residue 740 GLN Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 277 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 120 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 102 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 68 optimal weight: 0.0870 chunk 110 optimal weight: 0.0470 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 HIS A 727 HIS C 115 ASN C 186 ASN C 233 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.176365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.148667 restraints weight = 15841.289| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 2.48 r_work: 0.3726 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 10283 Z= 0.150 Angle : 0.657 12.820 13920 Z= 0.324 Chirality : 0.044 0.191 1603 Planarity : 0.005 0.047 1761 Dihedral : 4.154 18.331 1338 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.95 % Allowed : 22.57 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: 1.36 (0.25), residues: 1237 helix: 1.72 (0.21), residues: 628 sheet: 0.44 (0.39), residues: 194 loop : -0.02 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 121 TYR 0.020 0.002 TYR B 143 PHE 0.029 0.002 PHE C 113 TRP 0.010 0.001 TRP A 490 HIS 0.005 0.001 HIS A 727 Details of bonding type rmsd covalent geometry : bond 0.00364 (10283) covalent geometry : angle 0.65739 (13920) hydrogen bonds : bond 0.03775 ( 575) hydrogen bonds : angle 4.55233 ( 1761) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 239 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 SER cc_start: 0.7962 (t) cc_final: 0.7659 (t) REVERT: A 416 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7238 (mp0) REVERT: A 419 LYS cc_start: 0.8202 (ttpt) cc_final: 0.7879 (ttmp) REVERT: A 488 GLU cc_start: 0.7900 (tp30) cc_final: 0.7614 (mm-30) REVERT: A 574 ASP cc_start: 0.7585 (OUTLIER) cc_final: 0.7357 (t0) REVERT: A 584 GLU cc_start: 0.7169 (tm-30) cc_final: 0.6617 (tm-30) REVERT: A 590 MET cc_start: 0.8340 (mmm) cc_final: 0.7997 (tpt) REVERT: A 591 ASP cc_start: 0.7567 (t70) cc_final: 0.7288 (t0) REVERT: A 595 LYS cc_start: 0.8709 (tmmt) cc_final: 0.8271 (tttm) REVERT: A 630 LYS cc_start: 0.8008 (mttp) cc_final: 0.7687 (mtmm) REVERT: A 659 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.7078 (tm-30) REVERT: A 666 ASN cc_start: 0.7242 (t0) cc_final: 0.6920 (t0) REVERT: A 771 PHE cc_start: 0.8783 (m-80) cc_final: 0.8406 (m-80) REVERT: A 819 ARG cc_start: 0.7725 (mpp80) cc_final: 0.7305 (mpp80) REVERT: A 868 MET cc_start: 0.7373 (mtm) cc_final: 0.6272 (mtm) REVERT: B 29 LEU cc_start: 0.7865 (mm) cc_final: 0.7550 (mp) REVERT: B 122 LYS cc_start: 0.8071 (tmmt) cc_final: 0.7672 (tmmt) REVERT: C 14 LYS cc_start: 0.8529 (mtmt) cc_final: 0.8311 (mtmt) REVERT: C 42 THR cc_start: 0.8323 (m) cc_final: 0.7968 (p) REVERT: C 67 LYS cc_start: 0.7789 (mtmm) cc_final: 0.7571 (mtmm) REVERT: C 95 PHE cc_start: 0.8035 (m-80) cc_final: 0.7547 (m-80) REVERT: C 176 PHE cc_start: 0.8263 (p90) cc_final: 0.7899 (p90) REVERT: C 202 SER cc_start: 0.8774 (t) cc_final: 0.8542 (p) REVERT: C 285 LEU cc_start: 0.8702 (tp) cc_final: 0.8452 (tt) outliers start: 22 outliers final: 14 residues processed: 247 average time/residue: 0.4452 time to fit residues: 118.6888 Evaluate side-chains 249 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 233 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 532 HIS Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 652 GLN Chi-restraints excluded: chain A residue 659 GLU Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 725 TYR Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 196 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 75 optimal weight: 50.0000 chunk 24 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 41 optimal weight: 0.0370 chunk 95 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 39 optimal weight: 0.3980 chunk 94 optimal weight: 0.4980 chunk 110 optimal weight: 0.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 HIS A 727 HIS C 115 ASN C 233 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.175691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.147879 restraints weight = 15684.775| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 2.47 r_work: 0.3727 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 10283 Z= 0.157 Angle : 0.685 12.969 13920 Z= 0.335 Chirality : 0.044 0.165 1603 Planarity : 0.005 0.047 1761 Dihedral : 4.179 17.588 1338 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.42 % Allowed : 23.10 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: 1.37 (0.25), residues: 1237 helix: 1.70 (0.21), residues: 627 sheet: 0.43 (0.39), residues: 199 loop : 0.04 (0.32), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 121 TYR 0.020 0.002 TYR B 73 PHE 0.026 0.002 PHE C 113 TRP 0.008 0.001 TRP A 490 HIS 0.005 0.001 HIS A 596 Details of bonding type rmsd covalent geometry : bond 0.00384 (10283) covalent geometry : angle 0.68458 (13920) hydrogen bonds : bond 0.03907 ( 575) hydrogen bonds : angle 4.58297 ( 1761) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 239 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 SER cc_start: 0.7963 (t) cc_final: 0.7660 (t) REVERT: A 248 ARG cc_start: 0.7378 (tpt90) cc_final: 0.7036 (tpt90) REVERT: A 416 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7242 (mp0) REVERT: A 419 LYS cc_start: 0.8210 (ttpt) cc_final: 0.7887 (ttmp) REVERT: A 488 GLU cc_start: 0.7914 (tp30) cc_final: 0.7624 (mm-30) REVERT: A 574 ASP cc_start: 0.7627 (t70) cc_final: 0.7384 (t0) REVERT: A 584 GLU cc_start: 0.7174 (tm-30) cc_final: 0.6629 (tm-30) REVERT: A 590 MET cc_start: 0.8352 (mmm) cc_final: 0.8000 (tpt) REVERT: A 591 ASP cc_start: 0.7581 (t70) cc_final: 0.7298 (t0) REVERT: A 630 LYS cc_start: 0.8013 (mttp) cc_final: 0.7728 (mtmm) REVERT: A 659 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.7031 (tm-30) REVERT: A 666 ASN cc_start: 0.7245 (t0) cc_final: 0.6920 (t0) REVERT: A 684 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6794 (mm-30) REVERT: A 771 PHE cc_start: 0.8822 (m-80) cc_final: 0.8359 (m-80) REVERT: A 819 ARG cc_start: 0.7724 (mpp80) cc_final: 0.7295 (mpp80) REVERT: A 868 MET cc_start: 0.7362 (mtm) cc_final: 0.6282 (mtm) REVERT: B 29 LEU cc_start: 0.7860 (mm) cc_final: 0.7539 (mp) REVERT: B 122 LYS cc_start: 0.8062 (tmmt) cc_final: 0.7672 (tmmt) REVERT: C 14 LYS cc_start: 0.8532 (mtmt) cc_final: 0.8332 (mtmt) REVERT: C 42 THR cc_start: 0.8334 (m) cc_final: 0.8068 (p) REVERT: C 67 LYS cc_start: 0.7772 (mtmm) cc_final: 0.7541 (mtmm) REVERT: C 95 PHE cc_start: 0.7949 (m-80) cc_final: 0.7545 (m-80) REVERT: C 176 PHE cc_start: 0.8284 (p90) cc_final: 0.7972 (p90) REVERT: C 285 LEU cc_start: 0.8729 (tp) cc_final: 0.8472 (tt) outliers start: 16 outliers final: 12 residues processed: 245 average time/residue: 0.4349 time to fit residues: 115.6004 Evaluate side-chains 249 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 236 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 532 HIS Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 652 GLN Chi-restraints excluded: chain A residue 659 GLU Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 725 TYR Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 91 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 43 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 98 optimal weight: 0.0670 chunk 4 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 94 optimal weight: 0.0770 chunk 29 optimal weight: 0.2980 chunk 107 optimal weight: 0.7980 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 HIS A 727 HIS C 115 ASN C 233 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.175485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.147819 restraints weight = 15861.049| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 2.47 r_work: 0.3730 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 10283 Z= 0.152 Angle : 0.688 14.339 13920 Z= 0.335 Chirality : 0.044 0.166 1603 Planarity : 0.005 0.048 1761 Dihedral : 4.177 17.774 1338 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.77 % Allowed : 22.83 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: 1.40 (0.25), residues: 1237 helix: 1.70 (0.21), residues: 622 sheet: 0.42 (0.38), residues: 201 loop : 0.13 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 248 TYR 0.020 0.002 TYR B 73 PHE 0.030 0.002 PHE A 745 TRP 0.009 0.001 TRP A 490 HIS 0.005 0.001 HIS A 596 Details of bonding type rmsd covalent geometry : bond 0.00371 (10283) covalent geometry : angle 0.68836 (13920) hydrogen bonds : bond 0.03871 ( 575) hydrogen bonds : angle 4.57278 ( 1761) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3298.96 seconds wall clock time: 56 minutes 58.07 seconds (3418.07 seconds total)