Starting phenix.real_space_refine on Sat Oct 11 00:01:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8syo_40886/10_2025/8syo_40886.cif Found real_map, /net/cci-nas-00/data/ceres_data/8syo_40886/10_2025/8syo_40886.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/8syo_40886/10_2025/8syo_40886.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8syo_40886/10_2025/8syo_40886.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8syo_40886/10_2025/8syo_40886.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8syo_40886/10_2025/8syo_40886.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= 0.025 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-2.0-5842/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: 2.42, per 1000 atoms: 0.24 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: 0.77 Conformation dependent library (CDL) restraints added in 347.1 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: 0.40 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: 1.78 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 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: 1.710 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.620 Find NCS groups from input model: 0.050 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:6.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 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 352 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 ASP cc_start: 0.6920 (m-30) cc_final: 0.6653 (m-30) REVERT: A 123 GLU cc_start: 0.7404 (mp0) cc_final: 0.6885 (mp0) REVERT: A 344 MET cc_start: 0.8537 (mmt) cc_final: 0.8164 (mpp) REVERT: A 345 GLU cc_start: 0.7234 (pp20) cc_final: 0.6761 (pp20) REVERT: A 376 GLN cc_start: 0.6893 (tt0) cc_final: 0.6669 (mt0) REVERT: A 408 GLU cc_start: 0.7506 (tt0) cc_final: 0.6837 (tm-30) REVERT: A 416 GLU cc_start: 0.7041 (mp0) cc_final: 0.6501 (mp0) REVERT: A 420 LYS cc_start: 0.8060 (mtpp) cc_final: 0.7784 (mtpm) REVERT: A 488 GLU cc_start: 0.7844 (tp30) cc_final: 0.7200 (tm-30) REVERT: A 567 GLU cc_start: 0.7564 (mp0) cc_final: 0.6937 (mp0) REVERT: A 590 MET cc_start: 0.8216 (mmm) cc_final: 0.8012 (mmm) REVERT: A 591 ASP cc_start: 0.7362 (m-30) cc_final: 0.7149 (m-30) REVERT: A 599 GLU cc_start: 0.7649 (pm20) cc_final: 0.7391 (pp20) REVERT: A 615 LYS cc_start: 0.8094 (tppt) cc_final: 0.7671 (tptp) REVERT: A 652 GLN cc_start: 0.7667 (tp-100) cc_final: 0.7016 (tp-100) REVERT: A 655 SER cc_start: 0.8290 (m) cc_final: 0.7757 (p) REVERT: A 761 ILE cc_start: 0.8516 (mt) cc_final: 0.8111 (mt) REVERT: A 860 ASN cc_start: 0.7812 (t0) cc_final: 0.7551 (t0) REVERT: A 864 CYS cc_start: 0.7524 (m) cc_final: 0.7293 (m) REVERT: A 903 ASP cc_start: 0.7230 (t0) cc_final: 0.7019 (t0) REVERT: B 124 GLU cc_start: 0.7043 (mt-10) cc_final: 0.6597 (tt0) REVERT: B 165 VAL cc_start: 0.8022 (m) cc_final: 0.7546 (p) REVERT: C 20 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8284 (mt-10) REVERT: C 21 VAL cc_start: 0.8634 (t) cc_final: 0.8318 (p) REVERT: C 43 MET cc_start: 0.8870 (tmm) cc_final: 0.8492 (ttt) REVERT: C 50 GLN cc_start: 0.8293 (mm-40) cc_final: 0.7965 (mm-40) REVERT: C 112 VAL cc_start: 0.8775 (p) cc_final: 0.8535 (t) REVERT: C 113 PHE cc_start: 0.8487 (m-10) cc_final: 0.8190 (m-10) REVERT: C 175 LYS cc_start: 0.8177 (mppt) cc_final: 0.7931 (mppt) REVERT: C 200 GLU cc_start: 0.7407 (mt-10) cc_final: 0.7166 (mt-10) REVERT: C 201 SER cc_start: 0.8473 (p) cc_final: 0.8247 (m) REVERT: C 231 GLU cc_start: 0.7537 (pt0) cc_final: 0.7240 (pt0) outliers start: 0 outliers final: 0 residues processed: 352 average time/residue: 0.5875 time to fit residues: 221.9924 Evaluate side-chains 281 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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: 0.6980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 0.9980 chunk 123 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 ASN A 673 GLN ** A 792 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 HIS B 4 HIS B 72 ASN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 HIS C 115 ASN C 117 GLN C 183 ASN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.134112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.122356 restraints weight = 17553.340| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.42 r_work: 0.3598 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10283 Z= 0.189 Angle : 0.649 10.299 13920 Z= 0.331 Chirality : 0.046 0.212 1603 Planarity : 0.005 0.061 1761 Dihedral : 4.312 19.205 1338 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.81 % Allowed : 13.89 % Favored : 82.30 % 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: 1.17 (0.25), residues: 1237 helix: 1.44 (0.21), residues: 623 sheet: 0.53 (0.39), residues: 195 loop : 0.02 (0.33), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 766 TYR 0.033 0.002 TYR B 73 PHE 0.018 0.002 PHE A 796 TRP 0.011 0.001 TRP A 6 HIS 0.008 0.001 HIS A 789 Details of bonding type rmsd covalent geometry : bond 0.00434 (10283) covalent geometry : angle 0.64911 (13920) hydrogen bonds : bond 0.04450 ( 575) hydrogen bonds : angle 4.79573 ( 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 331 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 288 time to evaluate : 0.401 Fit side-chains REVERT: A 12 ASN cc_start: 0.8073 (t0) cc_final: 0.7830 (t0) REVERT: A 14 LYS cc_start: 0.8059 (ttmt) cc_final: 0.7741 (tmmt) REVERT: A 31 ASP cc_start: 0.7248 (m-30) cc_final: 0.6910 (m-30) REVERT: A 123 GLU cc_start: 0.7373 (mp0) cc_final: 0.6817 (mp0) REVERT: A 344 MET cc_start: 0.8639 (mmt) cc_final: 0.8250 (mpp) REVERT: A 345 GLU cc_start: 0.7276 (pp20) cc_final: 0.6742 (pp20) REVERT: A 366 LYS cc_start: 0.8377 (ptpp) cc_final: 0.7919 (tppt) REVERT: A 376 GLN cc_start: 0.7084 (tt0) cc_final: 0.6859 (mt0) REVERT: A 395 MET cc_start: 0.7803 (mtt) cc_final: 0.7535 (mtp) REVERT: A 416 GLU cc_start: 0.7027 (mp0) cc_final: 0.6560 (mp0) REVERT: A 420 LYS cc_start: 0.7945 (mtpp) cc_final: 0.7619 (mtpm) REVERT: A 488 GLU cc_start: 0.7849 (tp30) cc_final: 0.7428 (mm-30) REVERT: A 567 GLU cc_start: 0.7817 (mp0) cc_final: 0.7265 (mp0) REVERT: A 599 GLU cc_start: 0.7798 (pm20) cc_final: 0.7551 (pp20) REVERT: A 615 LYS cc_start: 0.8004 (tppt) cc_final: 0.7727 (tptp) REVERT: A 652 GLN cc_start: 0.7720 (tp-100) cc_final: 0.6645 (tp-100) REVERT: A 655 SER cc_start: 0.8221 (m) cc_final: 0.7830 (p) REVERT: A 722 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8504 (tp) REVERT: A 811 GLU cc_start: 0.6385 (tm-30) cc_final: 0.6156 (tm-30) REVERT: A 819 ARG cc_start: 0.7713 (mpp80) cc_final: 0.7495 (mpp80) REVERT: A 847 ASP cc_start: 0.7525 (p0) cc_final: 0.7319 (p0) REVERT: A 870 GLN cc_start: 0.8103 (mm-40) cc_final: 0.7322 (mm-40) REVERT: A 903 ASP cc_start: 0.7399 (t0) cc_final: 0.7187 (t0) REVERT: B 143 TYR cc_start: 0.8534 (p90) cc_final: 0.8254 (p90) REVERT: C 50 GLN cc_start: 0.8372 (mm-40) cc_final: 0.8048 (mm-40) REVERT: C 80 LYS cc_start: 0.8238 (mmmt) cc_final: 0.8036 (mmmt) REVERT: C 95 PHE cc_start: 0.8631 (m-80) cc_final: 0.8376 (m-80) REVERT: C 112 VAL cc_start: 0.8682 (p) cc_final: 0.8395 (t) REVERT: C 173 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8418 (mp) REVERT: C 175 LYS cc_start: 0.8303 (mppt) cc_final: 0.8000 (mppt) REVERT: C 203 GLU cc_start: 0.7940 (tt0) cc_final: 0.7716 (tt0) REVERT: C 231 GLU cc_start: 0.7504 (pt0) cc_final: 0.7240 (pt0) outliers start: 43 outliers final: 16 residues processed: 308 average time/residue: 0.6092 time to fit residues: 201.0554 Evaluate side-chains 266 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 248 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain B residue 4 HIS Chi-restraints excluded: chain B residue 43 ASN Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 177 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 122 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 93 optimal weight: 0.0570 chunk 34 optimal weight: 0.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 GLN ** A 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 ASN ** A 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 792 HIS A 806 GLN A 826 HIS ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN C 183 ASN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.132718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.121121 restraints weight = 17620.127| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.43 r_work: 0.3583 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10283 Z= 0.187 Angle : 0.643 12.379 13920 Z= 0.325 Chirality : 0.045 0.236 1603 Planarity : 0.004 0.052 1761 Dihedral : 4.349 19.061 1338 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.54 % Allowed : 18.85 % Favored : 77.61 % 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: 1.25 (0.25), residues: 1237 helix: 1.54 (0.21), residues: 625 sheet: 0.56 (0.39), residues: 192 loop : 0.01 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 126 TYR 0.032 0.002 TYR B 73 PHE 0.030 0.002 PHE A 358 TRP 0.016 0.001 TRP A 6 HIS 0.007 0.001 HIS B 128 Details of bonding type rmsd covalent geometry : bond 0.00442 (10283) covalent geometry : angle 0.64261 (13920) hydrogen bonds : bond 0.04160 ( 575) hydrogen bonds : angle 4.63597 ( 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 316 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 276 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.8086 (t0) cc_final: 0.7778 (t0) REVERT: A 14 LYS cc_start: 0.8013 (ttmt) cc_final: 0.7707 (tmmt) REVERT: A 31 ASP cc_start: 0.7245 (m-30) cc_final: 0.6909 (m-30) REVERT: A 123 GLU cc_start: 0.7400 (mp0) cc_final: 0.6844 (mp0) REVERT: A 239 ASP cc_start: 0.7309 (OUTLIER) cc_final: 0.7048 (m-30) REVERT: A 344 MET cc_start: 0.8594 (mmt) cc_final: 0.8255 (tpp) REVERT: A 376 GLN cc_start: 0.7074 (tt0) cc_final: 0.6841 (mt0) REVERT: A 416 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6644 (mp0) REVERT: A 590 MET cc_start: 0.8415 (mmm) cc_final: 0.7981 (tpp) REVERT: A 595 LYS cc_start: 0.8354 (tmmt) cc_final: 0.8070 (tmmt) REVERT: A 599 GLU cc_start: 0.7775 (pm20) cc_final: 0.7569 (pp20) REVERT: A 615 LYS cc_start: 0.8076 (tppt) cc_final: 0.7788 (tptp) REVERT: A 619 ASP cc_start: 0.7941 (m-30) cc_final: 0.7230 (m-30) REVERT: A 643 MET cc_start: 0.8432 (mmm) cc_final: 0.8181 (mmm) REVERT: A 655 SER cc_start: 0.8198 (m) cc_final: 0.7911 (p) REVERT: A 689 MET cc_start: 0.8008 (mtp) cc_final: 0.7762 (ttm) REVERT: A 707 TYR cc_start: 0.7913 (t80) cc_final: 0.7563 (t80) REVERT: A 766 ARG cc_start: 0.7684 (tpp80) cc_final: 0.7086 (mtt180) REVERT: A 788 ASP cc_start: 0.5427 (m-30) cc_final: 0.5032 (m-30) REVERT: A 806 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8152 (tp40) REVERT: A 811 GLU cc_start: 0.6470 (tm-30) cc_final: 0.6236 (tm-30) REVERT: A 836 TYR cc_start: 0.7804 (m-10) cc_final: 0.7495 (m-10) REVERT: A 847 ASP cc_start: 0.7501 (p0) cc_final: 0.7203 (p0) REVERT: A 870 GLN cc_start: 0.7816 (mm-40) cc_final: 0.7455 (mm-40) REVERT: A 873 GLU cc_start: 0.7070 (tm-30) cc_final: 0.6783 (pp20) REVERT: A 903 ASP cc_start: 0.7437 (t0) cc_final: 0.7219 (t70) REVERT: B 143 TYR cc_start: 0.8528 (p90) cc_final: 0.8297 (p90) REVERT: B 165 VAL cc_start: 0.8061 (OUTLIER) cc_final: 0.7703 (m) REVERT: C 43 MET cc_start: 0.8531 (tmm) cc_final: 0.8266 (ttp) REVERT: C 50 GLN cc_start: 0.8359 (mm-40) cc_final: 0.8046 (mm-40) REVERT: C 80 LYS cc_start: 0.8349 (mmmt) cc_final: 0.8092 (mmmt) REVERT: C 112 VAL cc_start: 0.8766 (p) cc_final: 0.8461 (t) REVERT: C 175 LYS cc_start: 0.8290 (mppt) cc_final: 0.7986 (mppt) REVERT: C 203 GLU cc_start: 0.7934 (tt0) cc_final: 0.7717 (tt0) REVERT: C 231 GLU cc_start: 0.7577 (pt0) cc_final: 0.7320 (pt0) REVERT: C 269 LYS cc_start: 0.8589 (mtmm) cc_final: 0.8202 (mtmm) outliers start: 40 outliers final: 15 residues processed: 297 average time/residue: 0.5728 time to fit residues: 182.8560 Evaluate side-chains 275 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 256 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 806 GLN Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 151 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 88 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 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 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 HIS B 4 HIS B 92 HIS ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN C 183 ASN C 233 GLN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.132092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.120438 restraints weight = 17669.028| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.46 r_work: 0.3581 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10283 Z= 0.184 Angle : 0.649 12.342 13920 Z= 0.323 Chirality : 0.045 0.237 1603 Planarity : 0.004 0.048 1761 Dihedral : 4.389 19.099 1338 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.45 % Allowed : 20.35 % Favored : 76.19 % 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: 1.23 (0.25), residues: 1237 helix: 1.55 (0.21), residues: 626 sheet: 0.55 (0.39), residues: 192 loop : -0.05 (0.32), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 819 TYR 0.030 0.002 TYR B 73 PHE 0.023 0.002 PHE A 796 TRP 0.016 0.001 TRP A 6 HIS 0.009 0.001 HIS B 90 Details of bonding type rmsd covalent geometry : bond 0.00434 (10283) covalent geometry : angle 0.64897 (13920) hydrogen bonds : bond 0.04019 ( 575) hydrogen bonds : angle 4.58441 ( 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 309 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 270 time to evaluate : 0.340 Fit side-chains REVERT: A 12 ASN cc_start: 0.8140 (t0) cc_final: 0.7853 (t0) REVERT: A 14 LYS cc_start: 0.8045 (ttmt) cc_final: 0.7699 (tmmt) REVERT: A 31 ASP cc_start: 0.7259 (m-30) cc_final: 0.6945 (m-30) REVERT: A 123 GLU cc_start: 0.7450 (mp0) cc_final: 0.7024 (mt-10) REVERT: A 376 GLN cc_start: 0.7107 (tt0) cc_final: 0.6871 (mt0) REVERT: A 416 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6680 (mp0) REVERT: A 561 SER cc_start: 0.8565 (m) cc_final: 0.8115 (t) REVERT: A 595 LYS cc_start: 0.8443 (tmmt) cc_final: 0.8171 (tmmt) REVERT: A 615 LYS cc_start: 0.8128 (tppt) cc_final: 0.7752 (tptp) REVERT: A 643 MET cc_start: 0.8449 (mmm) cc_final: 0.8127 (mmm) REVERT: A 652 GLN cc_start: 0.7821 (tp-100) cc_final: 0.6667 (tp-100) REVERT: A 655 SER cc_start: 0.8135 (m) cc_final: 0.7726 (p) REVERT: A 766 ARG cc_start: 0.7732 (tpp80) cc_final: 0.7136 (mtt90) REVERT: A 769 GLU cc_start: 0.8083 (tp30) cc_final: 0.7567 (tp30) REVERT: A 811 GLU cc_start: 0.6582 (OUTLIER) cc_final: 0.6342 (tm-30) REVERT: A 836 TYR cc_start: 0.7803 (m-10) cc_final: 0.7505 (m-10) REVERT: A 847 ASP cc_start: 0.7554 (p0) cc_final: 0.7172 (p0) REVERT: A 870 GLN cc_start: 0.7774 (mm-40) cc_final: 0.7322 (mm-40) REVERT: A 873 GLU cc_start: 0.7085 (tm-30) cc_final: 0.6791 (pp20) REVERT: B 143 TYR cc_start: 0.8519 (p90) cc_final: 0.8127 (p90) REVERT: B 158 ASP cc_start: 0.6584 (t70) cc_final: 0.6297 (t70) REVERT: B 165 VAL cc_start: 0.8052 (OUTLIER) cc_final: 0.7611 (m) REVERT: B 168 VAL cc_start: 0.8537 (p) cc_final: 0.8315 (m) REVERT: C 43 MET cc_start: 0.8571 (tmm) cc_final: 0.8332 (ttp) REVERT: C 50 GLN cc_start: 0.8422 (mm-40) cc_final: 0.8018 (mm-40) REVERT: C 62 PHE cc_start: 0.7512 (m-80) cc_final: 0.7291 (t80) REVERT: C 66 VAL cc_start: 0.8258 (m) cc_final: 0.7974 (p) REVERT: C 80 LYS cc_start: 0.8499 (mmmt) cc_final: 0.8224 (mmmt) REVERT: C 112 VAL cc_start: 0.8795 (p) cc_final: 0.8506 (t) REVERT: C 175 LYS cc_start: 0.8296 (mppt) cc_final: 0.8003 (mppt) REVERT: C 203 GLU cc_start: 0.7934 (tt0) cc_final: 0.7725 (tt0) REVERT: C 231 GLU cc_start: 0.7632 (pt0) cc_final: 0.7358 (pt0) REVERT: C 269 LYS cc_start: 0.8600 (mtmm) cc_final: 0.8218 (mtmm) outliers start: 39 outliers final: 20 residues processed: 291 average time/residue: 0.5807 time to fit residues: 181.1681 Evaluate side-chains 281 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 258 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 547 GLN Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain B residue 4 HIS Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 184 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 80 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 25 optimal weight: 0.4980 chunk 7 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 97 optimal weight: 0.0870 chunk 93 optimal weight: 0.4980 chunk 76 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 HIS ** A 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 ASN ** A 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 HIS ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN C 183 ASN C 234 ASN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.132268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.120597 restraints weight = 17670.937| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.48 r_work: 0.3574 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10283 Z= 0.157 Angle : 0.643 12.103 13920 Z= 0.318 Chirality : 0.044 0.216 1603 Planarity : 0.004 0.044 1761 Dihedral : 4.355 19.236 1338 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.98 % Allowed : 22.48 % Favored : 73.54 % 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: 1.28 (0.24), residues: 1237 helix: 1.62 (0.21), residues: 629 sheet: 0.53 (0.38), residues: 192 loop : -0.06 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 819 TYR 0.017 0.001 TYR A 707 PHE 0.033 0.002 PHE A 358 TRP 0.014 0.001 TRP A 6 HIS 0.008 0.001 HIS B 4 Details of bonding type rmsd covalent geometry : bond 0.00368 (10283) covalent geometry : angle 0.64334 (13920) hydrogen bonds : bond 0.03800 ( 575) hydrogen bonds : angle 4.52892 ( 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 305 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 260 time to evaluate : 0.394 Fit side-chains REVERT: A 7 HIS cc_start: 0.7586 (m90) cc_final: 0.7346 (m90) REVERT: A 12 ASN cc_start: 0.8135 (t0) cc_final: 0.7833 (t0) REVERT: A 14 LYS cc_start: 0.8059 (ttmt) cc_final: 0.7686 (tmmt) REVERT: A 31 ASP cc_start: 0.7149 (m-30) cc_final: 0.6891 (m-30) REVERT: A 123 GLU cc_start: 0.7400 (mp0) cc_final: 0.6953 (mt-10) REVERT: A 366 LYS cc_start: 0.8459 (ptpp) cc_final: 0.7913 (tppt) REVERT: A 376 GLN cc_start: 0.7096 (tt0) cc_final: 0.6850 (mt0) REVERT: A 395 MET cc_start: 0.7637 (mtt) cc_final: 0.7421 (mtp) REVERT: A 416 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6661 (mp0) REVERT: A 445 MET cc_start: 0.7816 (mmm) cc_final: 0.7614 (mmm) REVERT: A 561 SER cc_start: 0.8571 (m) cc_final: 0.8111 (t) REVERT: A 595 LYS cc_start: 0.8422 (tmmt) cc_final: 0.8097 (tmtt) REVERT: A 615 LYS cc_start: 0.8141 (tppt) cc_final: 0.7754 (tptp) REVERT: A 643 MET cc_start: 0.8390 (mmm) cc_final: 0.8049 (mmm) REVERT: A 652 GLN cc_start: 0.7761 (tp-100) cc_final: 0.6693 (tp-100) REVERT: A 655 SER cc_start: 0.8050 (m) cc_final: 0.7657 (p) REVERT: A 811 GLU cc_start: 0.6555 (OUTLIER) cc_final: 0.6296 (tm-30) REVERT: A 836 TYR cc_start: 0.7785 (m-10) cc_final: 0.7468 (m-10) REVERT: A 847 ASP cc_start: 0.7461 (p0) cc_final: 0.6981 (p0) REVERT: A 859 GLU cc_start: 0.7311 (tp30) cc_final: 0.6556 (tp30) REVERT: A 870 GLN cc_start: 0.7720 (mm-40) cc_final: 0.7141 (mm-40) REVERT: B 143 TYR cc_start: 0.8508 (p90) cc_final: 0.7981 (p90) REVERT: B 158 ASP cc_start: 0.6728 (t70) cc_final: 0.6416 (t70) REVERT: B 165 VAL cc_start: 0.8052 (OUTLIER) cc_final: 0.7591 (m) REVERT: B 168 VAL cc_start: 0.8479 (p) cc_final: 0.8263 (m) REVERT: C 13 ASN cc_start: 0.8522 (p0) cc_final: 0.8234 (p0) REVERT: C 43 MET cc_start: 0.8565 (tmm) cc_final: 0.8360 (ttp) REVERT: C 50 GLN cc_start: 0.8461 (mm-40) cc_final: 0.8057 (mm-40) REVERT: C 66 VAL cc_start: 0.8263 (m) cc_final: 0.7958 (p) REVERT: C 80 LYS cc_start: 0.8516 (mmmt) cc_final: 0.8220 (mmmt) REVERT: C 112 VAL cc_start: 0.8809 (p) cc_final: 0.8534 (t) REVERT: C 175 LYS cc_start: 0.8292 (mppt) cc_final: 0.7992 (mppt) REVERT: C 203 GLU cc_start: 0.7924 (tt0) cc_final: 0.7704 (tt0) REVERT: C 231 GLU cc_start: 0.7631 (pt0) cc_final: 0.7361 (pt0) outliers start: 45 outliers final: 19 residues processed: 285 average time/residue: 0.6030 time to fit residues: 184.2317 Evaluate side-chains 272 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 250 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 547 GLN Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 151 THR 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: 1.9990 chunk 54 optimal weight: 0.7980 chunk 106 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 123 optimal weight: 0.0040 chunk 83 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.6392 ------------------------------------------------------------------------------- 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 673 GLN ** A 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 HIS B 4 HIS ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 GLN C 73 ASN C 115 ASN C 183 ASN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.131546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.119920 restraints weight = 17666.793| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.47 r_work: 0.3575 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10283 Z= 0.175 Angle : 0.652 9.928 13920 Z= 0.324 Chirality : 0.045 0.236 1603 Planarity : 0.004 0.044 1761 Dihedral : 4.359 19.615 1338 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.63 % Allowed : 23.89 % Favored : 72.48 % 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: 1.28 (0.25), residues: 1237 helix: 1.61 (0.21), residues: 629 sheet: 0.58 (0.38), residues: 197 loop : -0.08 (0.33), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 819 TYR 0.016 0.001 TYR A 707 PHE 0.020 0.002 PHE A 796 TRP 0.016 0.001 TRP A 6 HIS 0.008 0.001 HIS B 90 Details of bonding type rmsd covalent geometry : bond 0.00411 (10283) covalent geometry : angle 0.65183 (13920) hydrogen bonds : bond 0.03875 ( 575) hydrogen bonds : angle 4.51352 ( 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 302 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 261 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: A 7 HIS cc_start: 0.7700 (m90) cc_final: 0.7453 (m90) REVERT: A 12 ASN cc_start: 0.8152 (t0) cc_final: 0.7862 (t0) REVERT: A 14 LYS cc_start: 0.8057 (ttmt) cc_final: 0.7678 (tmmt) REVERT: A 31 ASP cc_start: 0.7078 (m-30) cc_final: 0.6808 (m-30) REVERT: A 123 GLU cc_start: 0.7399 (mp0) cc_final: 0.6973 (mt-10) REVERT: A 288 ARG cc_start: 0.8166 (ttt180) cc_final: 0.7835 (ttt-90) REVERT: A 376 GLN cc_start: 0.7136 (tt0) cc_final: 0.6896 (mt0) REVERT: A 416 GLU cc_start: 0.7089 (OUTLIER) cc_final: 0.6732 (mp0) REVERT: A 561 SER cc_start: 0.8581 (m) cc_final: 0.8115 (t) REVERT: A 595 LYS cc_start: 0.8346 (tmmt) cc_final: 0.8056 (tmtt) REVERT: A 615 LYS cc_start: 0.8105 (tppt) cc_final: 0.7802 (tptp) REVERT: A 643 MET cc_start: 0.8445 (mmm) cc_final: 0.8108 (mmm) REVERT: A 655 SER cc_start: 0.8073 (m) cc_final: 0.7808 (p) REVERT: A 663 MET cc_start: 0.7718 (OUTLIER) cc_final: 0.7461 (tmm) REVERT: A 695 ARG cc_start: 0.7918 (mmm-85) cc_final: 0.7689 (mmm-85) REVERT: A 751 LEU cc_start: 0.8535 (tm) cc_final: 0.8306 (tt) REVERT: A 811 GLU cc_start: 0.6539 (OUTLIER) cc_final: 0.6293 (tm-30) REVERT: A 836 TYR cc_start: 0.7819 (m-10) cc_final: 0.7433 (m-10) REVERT: A 847 ASP cc_start: 0.7521 (p0) cc_final: 0.7061 (p0) REVERT: A 870 GLN cc_start: 0.7641 (mm-40) cc_final: 0.7165 (mm-40) REVERT: A 873 GLU cc_start: 0.7052 (tm-30) cc_final: 0.6710 (pp20) REVERT: B 122 LYS cc_start: 0.8264 (tmmt) cc_final: 0.7937 (tmmt) REVERT: B 143 TYR cc_start: 0.8504 (p90) cc_final: 0.7978 (p90) REVERT: B 158 ASP cc_start: 0.6755 (t70) cc_final: 0.6510 (t70) REVERT: B 168 VAL cc_start: 0.8466 (p) cc_final: 0.8253 (m) REVERT: C 13 ASN cc_start: 0.8557 (p0) cc_final: 0.8233 (p0) REVERT: C 66 VAL cc_start: 0.8262 (m) cc_final: 0.7968 (p) REVERT: C 80 LYS cc_start: 0.8575 (mmmt) cc_final: 0.8302 (mmmt) REVERT: C 112 VAL cc_start: 0.8786 (p) cc_final: 0.8571 (t) REVERT: C 175 LYS cc_start: 0.8305 (mppt) cc_final: 0.7998 (mppt) REVERT: C 203 GLU cc_start: 0.7921 (tt0) cc_final: 0.7691 (tt0) REVERT: C 210 GLU cc_start: 0.8158 (pt0) cc_final: 0.7643 (pt0) REVERT: C 231 GLU cc_start: 0.7645 (pt0) cc_final: 0.7373 (pt0) outliers start: 41 outliers final: 19 residues processed: 283 average time/residue: 0.5899 time to fit residues: 178.9667 Evaluate side-chains 273 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 251 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 547 GLN Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain B residue 4 HIS Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 184 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 117 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 71 optimal weight: 0.4980 chunk 70 optimal weight: 0.9980 chunk 115 optimal weight: 0.6980 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 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 ASN ** A 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 HIS B 4 HIS ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 GLN C 73 ASN C 115 ASN C 183 ASN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.131139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.119591 restraints weight = 17571.918| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.47 r_work: 0.3570 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10283 Z= 0.184 Angle : 0.668 13.485 13920 Z= 0.331 Chirality : 0.046 0.272 1603 Planarity : 0.004 0.045 1761 Dihedral : 4.384 19.659 1338 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.54 % Allowed : 25.40 % Favored : 71.06 % 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: 1.21 (0.24), residues: 1237 helix: 1.59 (0.21), residues: 628 sheet: 0.48 (0.37), residues: 197 loop : -0.15 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 819 TYR 0.015 0.002 TYR A 707 PHE 0.036 0.002 PHE A 358 TRP 0.013 0.001 TRP A 6 HIS 0.008 0.001 HIS B 4 Details of bonding type rmsd covalent geometry : bond 0.00435 (10283) covalent geometry : angle 0.66819 (13920) hydrogen bonds : bond 0.03923 ( 575) hydrogen bonds : angle 4.51485 ( 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 295 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 255 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: A 7 HIS cc_start: 0.7725 (m90) cc_final: 0.7462 (m90) REVERT: A 14 LYS cc_start: 0.8042 (ttmt) cc_final: 0.7689 (tmmt) REVERT: A 22 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.7019 (pt) REVERT: A 31 ASP cc_start: 0.7083 (m-30) cc_final: 0.6816 (m-30) REVERT: A 123 GLU cc_start: 0.7425 (mp0) cc_final: 0.7009 (mt-10) REVERT: A 376 GLN cc_start: 0.7161 (tt0) cc_final: 0.6916 (mt0) REVERT: A 395 MET cc_start: 0.7642 (mtt) cc_final: 0.7436 (mtp) REVERT: A 416 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6839 (mp0) REVERT: A 561 SER cc_start: 0.8589 (m) cc_final: 0.8108 (t) REVERT: A 615 LYS cc_start: 0.8123 (tppt) cc_final: 0.7755 (tptp) REVERT: A 663 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.7407 (tmm) REVERT: A 695 ARG cc_start: 0.7935 (mmm-85) cc_final: 0.7726 (mmm-85) REVERT: A 751 LEU cc_start: 0.8562 (tm) cc_final: 0.8317 (tt) REVERT: A 811 GLU cc_start: 0.6550 (OUTLIER) cc_final: 0.6308 (tm-30) REVERT: A 836 TYR cc_start: 0.7843 (m-10) cc_final: 0.7537 (m-10) REVERT: A 847 ASP cc_start: 0.7429 (p0) cc_final: 0.7016 (p0) REVERT: A 855 LYS cc_start: 0.8045 (mtpt) cc_final: 0.7272 (mppt) REVERT: A 870 GLN cc_start: 0.7595 (mm-40) cc_final: 0.6970 (mm-40) REVERT: A 873 GLU cc_start: 0.7028 (tm-30) cc_final: 0.6617 (pp20) REVERT: A 885 LYS cc_start: 0.8283 (pmtt) cc_final: 0.8056 (pmmt) REVERT: A 888 SER cc_start: 0.8156 (t) cc_final: 0.7900 (p) REVERT: B 122 LYS cc_start: 0.8294 (tmmt) cc_final: 0.7955 (tmmt) REVERT: B 143 TYR cc_start: 0.8498 (p90) cc_final: 0.7926 (p90) REVERT: B 157 MET cc_start: 0.7314 (OUTLIER) cc_final: 0.6940 (mtm) REVERT: B 158 ASP cc_start: 0.6888 (t70) cc_final: 0.6622 (t70) REVERT: C 13 ASN cc_start: 0.8553 (p0) cc_final: 0.8212 (p0) REVERT: C 14 LYS cc_start: 0.8546 (mtpm) cc_final: 0.8342 (mtmt) REVERT: C 52 SER cc_start: 0.7541 (t) cc_final: 0.7309 (m) REVERT: C 66 VAL cc_start: 0.8277 (m) cc_final: 0.7985 (p) REVERT: C 79 VAL cc_start: 0.8910 (t) cc_final: 0.8528 (m) REVERT: C 80 LYS cc_start: 0.8618 (mmmt) cc_final: 0.8356 (mmmt) REVERT: C 112 VAL cc_start: 0.8783 (p) cc_final: 0.8575 (t) outliers start: 40 outliers final: 25 residues processed: 280 average time/residue: 0.5924 time to fit residues: 177.7530 Evaluate side-chains 280 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 250 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 532 HIS Chi-restraints excluded: chain A residue 547 GLN Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain B residue 4 HIS Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 184 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 73 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 59 optimal weight: 0.4980 chunk 97 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 27 optimal weight: 0.3980 chunk 2 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN ** A 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 GLN A 666 ASN ** A 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 HIS ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 ASN C 70 GLN C 73 ASN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.131705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.120129 restraints weight = 17556.321| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.47 r_work: 0.3578 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10283 Z= 0.178 Angle : 0.684 11.517 13920 Z= 0.339 Chirality : 0.046 0.256 1603 Planarity : 0.004 0.044 1761 Dihedral : 4.415 19.518 1338 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.54 % Allowed : 25.93 % Favored : 70.53 % 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: 1.21 (0.24), residues: 1237 helix: 1.58 (0.21), residues: 628 sheet: 0.50 (0.37), residues: 197 loop : -0.15 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 819 TYR 0.015 0.001 TYR A 707 PHE 0.012 0.002 PHE A 894 TRP 0.012 0.001 TRP A 6 HIS 0.007 0.001 HIS B 90 Details of bonding type rmsd covalent geometry : bond 0.00426 (10283) covalent geometry : angle 0.68391 (13920) hydrogen bonds : bond 0.03886 ( 575) hydrogen bonds : angle 4.51959 ( 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 289 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 249 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: A 7 HIS cc_start: 0.7695 (m90) cc_final: 0.7436 (m90) REVERT: A 14 LYS cc_start: 0.8020 (ttmt) cc_final: 0.7675 (tmmt) REVERT: A 31 ASP cc_start: 0.7095 (m-30) cc_final: 0.6835 (m-30) REVERT: A 123 GLU cc_start: 0.7436 (mp0) cc_final: 0.7025 (mt-10) REVERT: A 288 ARG cc_start: 0.8159 (ttt180) cc_final: 0.7752 (ttt-90) REVERT: A 345 GLU cc_start: 0.7267 (pp20) cc_final: 0.6561 (pp20) REVERT: A 376 GLN cc_start: 0.7231 (tt0) cc_final: 0.6984 (mt0) REVERT: A 395 MET cc_start: 0.7602 (mtt) cc_final: 0.7389 (mtp) REVERT: A 416 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6849 (mp0) REVERT: A 567 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7300 (mm-30) REVERT: A 615 LYS cc_start: 0.8132 (tppt) cc_final: 0.7756 (tptp) REVERT: A 663 MET cc_start: 0.7675 (OUTLIER) cc_final: 0.7365 (tmm) REVERT: A 811 GLU cc_start: 0.6538 (OUTLIER) cc_final: 0.6294 (tm-30) REVERT: A 836 TYR cc_start: 0.7832 (m-10) cc_final: 0.7628 (m-10) REVERT: A 847 ASP cc_start: 0.7423 (p0) cc_final: 0.7076 (p0) REVERT: A 870 GLN cc_start: 0.7542 (mm-40) cc_final: 0.6912 (mm-40) REVERT: A 873 GLU cc_start: 0.7025 (tm-30) cc_final: 0.6605 (pp20) REVERT: A 885 LYS cc_start: 0.8257 (pmtt) cc_final: 0.8041 (pmmt) REVERT: A 888 SER cc_start: 0.8150 (t) cc_final: 0.7903 (p) REVERT: B 122 LYS cc_start: 0.8291 (tmmt) cc_final: 0.7952 (tmmt) REVERT: B 143 TYR cc_start: 0.8481 (p90) cc_final: 0.7909 (p90) REVERT: B 157 MET cc_start: 0.7366 (OUTLIER) cc_final: 0.6998 (mtm) REVERT: B 158 ASP cc_start: 0.6845 (t70) cc_final: 0.6576 (t70) REVERT: C 13 ASN cc_start: 0.8523 (p0) cc_final: 0.8191 (p0) REVERT: C 14 LYS cc_start: 0.8537 (mtpm) cc_final: 0.8325 (mtmt) REVERT: C 52 SER cc_start: 0.7519 (t) cc_final: 0.7285 (m) REVERT: C 66 VAL cc_start: 0.8257 (m) cc_final: 0.7958 (p) REVERT: C 79 VAL cc_start: 0.8922 (t) cc_final: 0.8551 (m) REVERT: C 80 LYS cc_start: 0.8631 (mmmt) cc_final: 0.8381 (mmmt) REVERT: C 112 VAL cc_start: 0.8764 (p) cc_final: 0.8560 (t) outliers start: 40 outliers final: 21 residues processed: 271 average time/residue: 0.6335 time to fit residues: 182.9501 Evaluate side-chains 270 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 245 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 532 HIS Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain B residue 4 HIS Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 172 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 120 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 chunk 3 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 102 optimal weight: 0.1980 chunk 6 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 110 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN ** A 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 ASN ** A 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 ASN C 70 GLN C 73 ASN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.132274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.120583 restraints weight = 17535.247| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.49 r_work: 0.3569 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10283 Z= 0.165 Angle : 0.689 14.340 13920 Z= 0.339 Chirality : 0.046 0.241 1603 Planarity : 0.004 0.044 1761 Dihedral : 4.412 19.499 1338 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.36 % Allowed : 26.46 % Favored : 70.18 % 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: 1.21 (0.25), residues: 1237 helix: 1.58 (0.21), residues: 628 sheet: 0.50 (0.38), residues: 197 loop : -0.15 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 819 TYR 0.015 0.001 TYR A 707 PHE 0.042 0.002 PHE A 358 TRP 0.010 0.001 TRP A 490 HIS 0.006 0.001 HIS B 90 Details of bonding type rmsd covalent geometry : bond 0.00396 (10283) covalent geometry : angle 0.68937 (13920) hydrogen bonds : bond 0.03818 ( 575) hydrogen bonds : angle 4.51294 ( 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 290 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 252 time to evaluate : 0.430 Fit side-chains REVERT: A 7 HIS cc_start: 0.7685 (m90) cc_final: 0.7421 (m90) REVERT: A 14 LYS cc_start: 0.8021 (ttmt) cc_final: 0.7677 (tmmt) REVERT: A 31 ASP cc_start: 0.7097 (m-30) cc_final: 0.6815 (m-30) REVERT: A 123 GLU cc_start: 0.7435 (mp0) cc_final: 0.7010 (mt-10) REVERT: A 288 ARG cc_start: 0.8166 (ttt180) cc_final: 0.7757 (ttt-90) REVERT: A 345 GLU cc_start: 0.7256 (pp20) cc_final: 0.6799 (pp20) REVERT: A 376 GLN cc_start: 0.7217 (tt0) cc_final: 0.6980 (mt0) REVERT: A 416 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6865 (mp0) REVERT: A 567 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7288 (mm-30) REVERT: A 595 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.8067 (tmmt) REVERT: A 610 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7745 (mp) REVERT: A 615 LYS cc_start: 0.8255 (tppt) cc_final: 0.7845 (tptp) REVERT: A 663 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.7419 (tmm) REVERT: A 724 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.8040 (mp) REVERT: A 751 LEU cc_start: 0.8482 (tm) cc_final: 0.8267 (tt) REVERT: A 754 GLU cc_start: 0.8082 (tp30) cc_final: 0.7575 (tm-30) REVERT: A 811 GLU cc_start: 0.6547 (OUTLIER) cc_final: 0.6285 (tm-30) REVERT: A 847 ASP cc_start: 0.7356 (p0) cc_final: 0.7039 (p0) REVERT: A 870 GLN cc_start: 0.7517 (mm-40) cc_final: 0.6864 (mm-40) REVERT: A 873 GLU cc_start: 0.7053 (tm-30) cc_final: 0.6729 (pp20) REVERT: A 885 LYS cc_start: 0.8252 (pmtt) cc_final: 0.8022 (pmmt) REVERT: A 888 SER cc_start: 0.8047 (t) cc_final: 0.7808 (p) REVERT: B 122 LYS cc_start: 0.8227 (tmmt) cc_final: 0.7919 (tmmt) REVERT: B 143 TYR cc_start: 0.8472 (p90) cc_final: 0.7831 (p90) REVERT: B 157 MET cc_start: 0.7368 (OUTLIER) cc_final: 0.7032 (mtm) REVERT: C 13 ASN cc_start: 0.8506 (p0) cc_final: 0.8168 (p0) REVERT: C 14 LYS cc_start: 0.8507 (mtpm) cc_final: 0.8286 (mtmt) REVERT: C 52 SER cc_start: 0.7838 (t) cc_final: 0.7576 (m) REVERT: C 66 VAL cc_start: 0.8286 (m) cc_final: 0.7982 (p) REVERT: C 79 VAL cc_start: 0.8917 (t) cc_final: 0.8551 (m) REVERT: C 80 LYS cc_start: 0.8642 (mmmt) cc_final: 0.8398 (mmmt) REVERT: C 228 ASP cc_start: 0.7515 (p0) cc_final: 0.7170 (p0) outliers start: 38 outliers final: 21 residues processed: 276 average time/residue: 0.6151 time to fit residues: 181.7224 Evaluate side-chains 279 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 251 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 532 HIS Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 184 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 75 optimal weight: 0.4980 chunk 24 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 58 optimal weight: 0.3980 chunk 39 optimal weight: 0.5980 chunk 94 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN A 369 HIS ** A 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 ASN ** A 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 ASN C 70 GLN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.131886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.120363 restraints weight = 17463.690| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.47 r_work: 0.3582 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10283 Z= 0.175 Angle : 0.725 14.762 13920 Z= 0.357 Chirality : 0.046 0.236 1603 Planarity : 0.004 0.045 1761 Dihedral : 4.467 19.335 1338 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.27 % Allowed : 27.17 % Favored : 69.56 % 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: 1.19 (0.25), residues: 1237 helix: 1.56 (0.21), residues: 628 sheet: 0.48 (0.37), residues: 197 loop : -0.14 (0.33), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 819 TYR 0.015 0.002 TYR B 73 PHE 0.041 0.002 PHE A 358 TRP 0.009 0.001 TRP A 490 HIS 0.006 0.001 HIS B 90 Details of bonding type rmsd covalent geometry : bond 0.00419 (10283) covalent geometry : angle 0.72450 (13920) hydrogen bonds : bond 0.03937 ( 575) hydrogen bonds : angle 4.55603 ( 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 292 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 255 time to evaluate : 0.388 Fit side-chains REVERT: A 7 HIS cc_start: 0.7741 (m90) cc_final: 0.7532 (m90) REVERT: A 14 LYS cc_start: 0.7974 (ttmt) cc_final: 0.7630 (tmmt) REVERT: A 31 ASP cc_start: 0.7058 (m-30) cc_final: 0.6810 (m-30) REVERT: A 123 GLU cc_start: 0.7422 (mp0) cc_final: 0.7014 (mt-10) REVERT: A 202 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.7630 (t70) REVERT: A 248 ARG cc_start: 0.7083 (tpt90) cc_final: 0.6352 (tpt170) REVERT: A 288 ARG cc_start: 0.8142 (ttt180) cc_final: 0.7738 (ttt-90) REVERT: A 345 GLU cc_start: 0.7313 (pp20) cc_final: 0.6807 (pp20) REVERT: A 376 GLN cc_start: 0.7259 (tt0) cc_final: 0.7025 (mt0) REVERT: A 416 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6835 (mp0) REVERT: A 567 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7314 (mm-30) REVERT: A 595 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.8062 (tmmt) REVERT: A 610 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7726 (mp) REVERT: A 615 LYS cc_start: 0.8199 (tppt) cc_final: 0.7811 (tptp) REVERT: A 663 MET cc_start: 0.7646 (OUTLIER) cc_final: 0.7395 (tmm) REVERT: A 724 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.8017 (mp) REVERT: A 811 GLU cc_start: 0.6581 (OUTLIER) cc_final: 0.6320 (tm-30) REVERT: A 817 LYS cc_start: 0.7182 (ttmm) cc_final: 0.6912 (ttmt) REVERT: A 885 LYS cc_start: 0.8246 (pmtt) cc_final: 0.8041 (pmmt) REVERT: A 888 SER cc_start: 0.8050 (t) cc_final: 0.7809 (p) REVERT: B 122 LYS cc_start: 0.8268 (tmmt) cc_final: 0.7936 (tmmt) REVERT: B 143 TYR cc_start: 0.8480 (p90) cc_final: 0.7962 (p90) REVERT: B 180 ARG cc_start: 0.8201 (mtp-110) cc_final: 0.7968 (mtp85) REVERT: C 13 ASN cc_start: 0.8499 (p0) cc_final: 0.8181 (p0) REVERT: C 52 SER cc_start: 0.7796 (t) cc_final: 0.7553 (m) REVERT: C 66 VAL cc_start: 0.8250 (m) cc_final: 0.7949 (p) REVERT: C 79 VAL cc_start: 0.8918 (t) cc_final: 0.8547 (m) REVERT: C 80 LYS cc_start: 0.8624 (mmmt) cc_final: 0.8374 (mmmt) REVERT: C 217 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7407 (mt-10) REVERT: C 228 ASP cc_start: 0.7472 (p0) cc_final: 0.7129 (p0) REVERT: C 269 LYS cc_start: 0.8354 (mtmm) cc_final: 0.8088 (mtmm) outliers start: 37 outliers final: 21 residues processed: 271 average time/residue: 0.6463 time to fit residues: 187.2211 Evaluate side-chains 274 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 246 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 532 HIS Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 184 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 43 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 chunk 94 optimal weight: 0.0370 chunk 29 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- 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 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 ASN ** A 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 HIS A 870 GLN B 4 HIS B 36 GLN ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 ASN C 70 GLN C 73 ASN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.131340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.119920 restraints weight = 17737.220| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.49 r_work: 0.3567 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10283 Z= 0.191 Angle : 0.747 14.812 13920 Z= 0.365 Chirality : 0.047 0.226 1603 Planarity : 0.005 0.046 1761 Dihedral : 4.491 19.186 1338 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.27 % Allowed : 27.70 % Favored : 69.03 % 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: 1.11 (0.24), residues: 1237 helix: 1.47 (0.21), residues: 628 sheet: 0.45 (0.37), residues: 197 loop : -0.12 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 819 TYR 0.016 0.002 TYR B 73 PHE 0.042 0.002 PHE A 358 TRP 0.009 0.001 TRP A 490 HIS 0.007 0.001 HIS B 90 Details of bonding type rmsd covalent geometry : bond 0.00459 (10283) covalent geometry : angle 0.74697 (13920) hydrogen bonds : bond 0.04025 ( 575) hydrogen bonds : angle 4.62340 ( 1761) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3843.26 seconds wall clock time: 66 minutes 23.37 seconds (3983.37 seconds total)