Starting phenix.real_space_refine on Fri Feb 14 09:31:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8syn_40885/02_2025/8syn_40885.cif Found real_map, /net/cci-nas-00/data/ceres_data/8syn_40885/02_2025/8syn_40885.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8syn_40885/02_2025/8syn_40885.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8syn_40885/02_2025/8syn_40885.map" model { file = "/net/cci-nas-00/data/ceres_data/8syn_40885/02_2025/8syn_40885.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8syn_40885/02_2025/8syn_40885.cif" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 6487 2.51 5 N 1695 2.21 5 O 1825 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 6.16, per 1000 atoms: 0.61 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: 2.61 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.15 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: 3.27 Time building geometry restraints manager: 3.08 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: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 25.360 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:12.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 10283 Z= 0.253 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.011 0.001 TRP A 490 HIS 0.014 0.001 HIS A 596 PHE 0.024 0.002 PHE C 93 TYR 0.041 0.002 TYR A 821 ARG 0.003 0.000 ARG A 318 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 LYS cc_start: 0.7396 (tttt) cc_final: 0.7129 (tttp) REVERT: A 344 MET cc_start: 0.8505 (mmt) cc_final: 0.8076 (mpp) REVERT: A 366 LYS cc_start: 0.7729 (tptp) cc_final: 0.7400 (tppt) REVERT: A 488 GLU cc_start: 0.7811 (tp30) cc_final: 0.7489 (mm-30) REVERT: A 514 CYS cc_start: 0.7977 (m) cc_final: 0.7600 (m) REVERT: A 584 GLU cc_start: 0.6888 (tm-30) cc_final: 0.6471 (tm-30) REVERT: A 595 LYS cc_start: 0.8420 (tmmt) cc_final: 0.8215 (tmmm) REVERT: A 599 GLU cc_start: 0.7619 (pm20) cc_final: 0.7386 (mp0) REVERT: A 630 LYS cc_start: 0.7670 (mttp) cc_final: 0.7330 (mtmm) REVERT: A 659 GLU cc_start: 0.6575 (pp20) cc_final: 0.6102 (tm-30) REVERT: A 868 MET cc_start: 0.5468 (mtm) cc_final: 0.4972 (mtm) REVERT: B 43 ASN cc_start: 0.7578 (m110) cc_final: 0.7253 (m110) REVERT: C 14 LYS cc_start: 0.8518 (mtmt) cc_final: 0.8299 (mtmt) REVERT: C 44 GLU cc_start: 0.8046 (tt0) cc_final: 0.7820 (tt0) REVERT: C 175 LYS cc_start: 0.8205 (mppt) cc_final: 0.7831 (mppt) REVERT: C 176 PHE cc_start: 0.7972 (p90) cc_final: 0.7755 (p90) REVERT: C 231 GLU cc_start: 0.7546 (pt0) cc_final: 0.7304 (pt0) REVERT: C 269 LYS cc_start: 0.8207 (mtmm) cc_final: 0.7895 (mtmm) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 1.2098 time to fit residues: 343.5451 Evaluate side-chains 238 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 0.5980 chunk 94 optimal weight: 0.4980 chunk 52 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 63 optimal weight: 0.0770 chunk 50 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 37 optimal weight: 0.0670 chunk 59 optimal weight: 0.0570 chunk 72 optimal weight: 30.0000 chunk 113 optimal weight: 0.6980 overall best weight: 0.2594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 727 HIS A 778 ASN C 115 ASN C 117 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.176487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.149111 restraints weight = 15634.820| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 2.43 r_work: 0.3751 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 10283 Z= 0.210 Angle : 0.604 8.179 13920 Z= 0.309 Chirality : 0.044 0.144 1603 Planarity : 0.004 0.061 1761 Dihedral : 4.269 19.212 1338 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.68 % Allowed : 10.18 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.25), residues: 1237 helix: 1.60 (0.21), residues: 624 sheet: 0.48 (0.39), residues: 197 loop : 0.05 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 810 HIS 0.009 0.001 HIS B 90 PHE 0.025 0.002 PHE A 796 TYR 0.028 0.002 TYR B 73 ARG 0.006 0.000 ARG A 819 *********************** 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 269 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 250 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 ASP cc_start: 0.7684 (t0) cc_final: 0.7421 (t0) REVERT: A 344 MET cc_start: 0.8695 (mmt) cc_final: 0.8331 (tpp) REVERT: A 366 LYS cc_start: 0.7833 (tptp) cc_final: 0.7547 (tppt) REVERT: A 395 MET cc_start: 0.8091 (mtt) cc_final: 0.7890 (mtp) REVERT: A 419 LYS cc_start: 0.8130 (ttpt) cc_final: 0.7878 (ttmt) REVERT: A 488 GLU cc_start: 0.7650 (tp30) cc_final: 0.7377 (mm-30) REVERT: A 514 CYS cc_start: 0.7846 (m) cc_final: 0.7485 (m) REVERT: A 584 GLU cc_start: 0.7144 (tm-30) cc_final: 0.6700 (tm-30) REVERT: A 595 LYS cc_start: 0.8739 (tmmt) cc_final: 0.8305 (tmmm) REVERT: A 596 HIS cc_start: 0.8303 (m170) cc_final: 0.8081 (m-70) REVERT: A 630 LYS cc_start: 0.7890 (mttp) cc_final: 0.7679 (mtmm) REVERT: A 652 GLN cc_start: 0.7056 (OUTLIER) cc_final: 0.6737 (tp-100) REVERT: A 659 GLU cc_start: 0.6654 (pp20) cc_final: 0.6182 (tm-30) REVERT: A 661 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7863 (ttm110) REVERT: A 684 GLU cc_start: 0.7233 (mt-10) cc_final: 0.6906 (mm-30) REVERT: A 868 MET cc_start: 0.7420 (mtm) cc_final: 0.6290 (mtm) REVERT: B 12 ASP cc_start: 0.8332 (m-30) cc_final: 0.8124 (m-30) REVERT: B 176 VAL cc_start: 0.8077 (OUTLIER) cc_final: 0.7819 (m) REVERT: C 14 LYS cc_start: 0.8599 (mtmt) cc_final: 0.8354 (mtmt) REVERT: C 43 MET cc_start: 0.7993 (tmm) cc_final: 0.7704 (ttm) REVERT: C 175 LYS cc_start: 0.8112 (mppt) cc_final: 0.7722 (mppt) REVERT: C 269 LYS cc_start: 0.8215 (mtmm) cc_final: 0.7926 (mtmm) outliers start: 19 outliers final: 8 residues processed: 258 average time/residue: 1.0784 time to fit residues: 301.5200 Evaluate side-chains 240 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 229 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 652 GLN Chi-restraints excluded: chain A residue 661 ARG Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 289 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 97 optimal weight: 1.9990 chunk 2 optimal weight: 0.0000 chunk 71 optimal weight: 0.6980 chunk 94 optimal weight: 0.0170 chunk 36 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 69 optimal weight: 0.0060 chunk 100 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 110 optimal weight: 0.0570 overall best weight: 0.1556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 516 HIS A 727 HIS ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN C 186 ASN C 233 GLN C 234 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.177444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.150210 restraints weight = 15865.532| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 2.44 r_work: 0.3770 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10283 Z= 0.177 Angle : 0.577 9.138 13920 Z= 0.294 Chirality : 0.043 0.161 1603 Planarity : 0.004 0.051 1761 Dihedral : 4.161 18.409 1338 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.04 % Allowed : 13.45 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.25), residues: 1237 helix: 1.79 (0.21), residues: 628 sheet: 0.52 (0.40), residues: 192 loop : 0.07 (0.32), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 490 HIS 0.006 0.001 HIS B 90 PHE 0.037 0.002 PHE A 796 TYR 0.027 0.002 TYR B 73 ARG 0.007 0.000 ARG A 819 *********************** 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 265 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 242 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 SER cc_start: 0.7982 (t) cc_final: 0.7701 (t) REVERT: A 366 LYS cc_start: 0.7830 (tptp) cc_final: 0.7553 (tppt) REVERT: A 419 LYS cc_start: 0.8122 (ttpt) cc_final: 0.7899 (ttmt) REVERT: A 488 GLU cc_start: 0.7674 (tp30) cc_final: 0.7406 (mm-30) REVERT: A 574 ASP cc_start: 0.7515 (t70) cc_final: 0.7273 (t0) REVERT: A 584 GLU cc_start: 0.7028 (tm-30) cc_final: 0.6584 (tm-30) REVERT: A 630 LYS cc_start: 0.7899 (mttp) cc_final: 0.7664 (mtmm) REVERT: A 659 GLU cc_start: 0.6661 (pp20) cc_final: 0.6268 (tm-30) REVERT: A 683 MET cc_start: 0.7814 (mmm) cc_final: 0.7584 (mmp) REVERT: A 684 GLU cc_start: 0.7255 (mt-10) cc_final: 0.6887 (mm-30) REVERT: A 800 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7383 (mp0) REVERT: A 819 ARG cc_start: 0.7650 (mpp80) cc_final: 0.7444 (mpp80) REVERT: A 868 MET cc_start: 0.7459 (mtm) cc_final: 0.6331 (mtm) REVERT: B 122 LYS cc_start: 0.8075 (tmmt) cc_final: 0.7727 (tmmt) REVERT: B 131 LYS cc_start: 0.7664 (mmmt) cc_final: 0.7312 (mmmm) REVERT: B 133 TYR cc_start: 0.7664 (m-80) cc_final: 0.7413 (m-80) REVERT: B 176 VAL cc_start: 0.8062 (OUTLIER) cc_final: 0.7805 (m) REVERT: C 14 LYS cc_start: 0.8587 (mtmt) cc_final: 0.8370 (mtmt) REVERT: C 43 MET cc_start: 0.7982 (tmm) cc_final: 0.7729 (ttm) REVERT: C 175 LYS cc_start: 0.8061 (mppt) cc_final: 0.7632 (mppt) REVERT: C 269 LYS cc_start: 0.8163 (mtmm) cc_final: 0.7878 (mtmm) outliers start: 23 outliers final: 10 residues processed: 252 average time/residue: 1.1921 time to fit residues: 324.1468 Evaluate side-chains 247 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 235 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 196 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 60 optimal weight: 0.3980 chunk 0 optimal weight: 80.0000 chunk 78 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 ASN B 170 GLN C 115 ASN C 186 ASN C 233 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.171746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.143837 restraints weight = 15857.938| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 2.43 r_work: 0.3667 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.081 10283 Z= 0.529 Angle : 0.703 11.831 13920 Z= 0.361 Chirality : 0.049 0.181 1603 Planarity : 0.005 0.055 1761 Dihedral : 4.545 18.928 1338 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.83 % Allowed : 15.93 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.24), residues: 1237 helix: 1.42 (0.20), residues: 625 sheet: 0.24 (0.37), residues: 210 loop : 0.03 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 199 HIS 0.007 0.001 HIS C 142 PHE 0.042 0.003 PHE A 796 TYR 0.031 0.003 TYR B 73 ARG 0.005 0.001 ARG C 11 *********************** 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 280 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 248 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7453 (mp0) REVERT: A 202 ASP cc_start: 0.7974 (OUTLIER) cc_final: 0.7578 (t0) REVERT: A 249 ILE cc_start: 0.8434 (mp) cc_final: 0.8229 (mt) REVERT: A 395 MET cc_start: 0.8160 (mtt) cc_final: 0.7919 (mtp) REVERT: A 417 ARG cc_start: 0.7998 (tpp80) cc_final: 0.7785 (ttm170) REVERT: A 419 LYS cc_start: 0.8199 (ttpt) cc_final: 0.7947 (ttmt) REVERT: A 488 GLU cc_start: 0.7941 (tp30) cc_final: 0.7672 (mm-30) REVERT: A 514 CYS cc_start: 0.7797 (m) cc_final: 0.7514 (m) REVERT: A 567 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7446 (mp0) REVERT: A 574 ASP cc_start: 0.7610 (t70) cc_final: 0.7376 (t0) REVERT: A 595 LYS cc_start: 0.8762 (tmmm) cc_final: 0.8308 (tttm) REVERT: A 630 LYS cc_start: 0.8109 (mttp) cc_final: 0.7849 (mtmm) REVERT: A 637 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8743 (mp) REVERT: A 643 MET cc_start: 0.8447 (mmm) cc_final: 0.8086 (mmt) REVERT: A 659 GLU cc_start: 0.6971 (pp20) cc_final: 0.6513 (tm-30) REVERT: A 661 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7827 (ttm110) REVERT: A 666 ASN cc_start: 0.7667 (t0) cc_final: 0.7407 (t0) REVERT: A 686 ARG cc_start: 0.7298 (tmm160) cc_final: 0.6584 (tmm160) REVERT: A 712 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.8106 (mp) REVERT: A 800 GLU cc_start: 0.8366 (mp0) cc_final: 0.7642 (mp0) REVERT: A 819 ARG cc_start: 0.7597 (mpp80) cc_final: 0.7225 (mpp80) REVERT: A 868 MET cc_start: 0.7399 (mtm) cc_final: 0.6300 (mtm) REVERT: B 133 TYR cc_start: 0.7798 (m-80) cc_final: 0.7495 (m-80) REVERT: C 43 MET cc_start: 0.8084 (tmm) cc_final: 0.7848 (ttm) REVERT: C 95 PHE cc_start: 0.8337 (m-80) cc_final: 0.8085 (m-80) REVERT: C 175 LYS cc_start: 0.8108 (mppt) cc_final: 0.7830 (mppt) REVERT: C 176 PHE cc_start: 0.8390 (p90) cc_final: 0.8142 (p90) REVERT: C 203 GLU cc_start: 0.7787 (tt0) cc_final: 0.7118 (tt0) REVERT: C 269 LYS cc_start: 0.8244 (mtmm) cc_final: 0.7946 (mtmm) outliers start: 32 outliers final: 13 residues processed: 257 average time/residue: 1.2014 time to fit residues: 332.0580 Evaluate side-chains 259 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 241 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 661 ARG Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 217 GLU Chi-restraints excluded: chain C residue 277 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 67 optimal weight: 0.0770 chunk 101 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 76 optimal weight: 30.0000 chunk 59 optimal weight: 0.6980 chunk 115 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 727 HIS A 911 GLN C 115 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.174590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.146959 restraints weight = 15696.418| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 2.45 r_work: 0.3718 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10283 Z= 0.258 Angle : 0.622 11.037 13920 Z= 0.314 Chirality : 0.044 0.154 1603 Planarity : 0.004 0.048 1761 Dihedral : 4.330 18.528 1338 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.19 % Allowed : 17.88 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.25), residues: 1237 helix: 1.70 (0.21), residues: 624 sheet: 0.25 (0.38), residues: 199 loop : 0.10 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 490 HIS 0.005 0.001 HIS B 90 PHE 0.032 0.002 PHE A 796 TYR 0.032 0.002 TYR B 73 ARG 0.006 0.000 ARG A 121 *********************** 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 278 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 242 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 417 ARG cc_start: 0.7966 (tpp80) cc_final: 0.7758 (ttm170) REVERT: A 419 LYS cc_start: 0.8178 (ttpt) cc_final: 0.7948 (ttmt) REVERT: A 488 GLU cc_start: 0.7867 (tp30) cc_final: 0.7584 (mm-30) REVERT: A 574 ASP cc_start: 0.7567 (OUTLIER) cc_final: 0.7317 (t0) REVERT: A 584 GLU cc_start: 0.7507 (tp30) cc_final: 0.6932 (tm-30) REVERT: A 630 LYS cc_start: 0.8071 (mttp) cc_final: 0.7791 (mtmm) REVERT: A 637 ILE cc_start: 0.8958 (OUTLIER) cc_final: 0.8753 (mp) REVERT: A 643 MET cc_start: 0.8346 (mmm) cc_final: 0.7989 (mmt) REVERT: A 659 GLU cc_start: 0.6942 (pp20) cc_final: 0.6522 (tm-30) REVERT: A 661 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7722 (ttm110) REVERT: A 666 ASN cc_start: 0.7539 (t0) cc_final: 0.7260 (t0) REVERT: A 686 ARG cc_start: 0.7201 (tmm160) cc_final: 0.6544 (tmm160) REVERT: A 800 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7543 (mp0) REVERT: A 819 ARG cc_start: 0.7742 (mpp80) cc_final: 0.7497 (mpp80) REVERT: A 868 MET cc_start: 0.7364 (mtm) cc_final: 0.6261 (mtm) REVERT: B 89 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.8178 (pp) REVERT: B 122 LYS cc_start: 0.8140 (tmmt) cc_final: 0.7614 (tmmt) REVERT: B 133 TYR cc_start: 0.7780 (m-80) cc_final: 0.7537 (m-80) REVERT: C 14 LYS cc_start: 0.8593 (mtmt) cc_final: 0.8377 (mtmt) REVERT: C 43 MET cc_start: 0.8071 (tmm) cc_final: 0.7835 (ttm) REVERT: C 95 PHE cc_start: 0.8279 (m-80) cc_final: 0.7999 (m-80) REVERT: C 176 PHE cc_start: 0.8382 (p90) cc_final: 0.8074 (p90) REVERT: C 269 LYS cc_start: 0.8211 (mtmm) cc_final: 0.7930 (mtmm) REVERT: C 290 PHE cc_start: 0.8302 (m-80) cc_final: 0.8088 (m-80) outliers start: 36 outliers final: 20 residues processed: 257 average time/residue: 1.2193 time to fit residues: 340.2611 Evaluate side-chains 264 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 239 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 532 HIS Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 652 GLN Chi-restraints excluded: chain A residue 661 ARG Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 217 GLU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 277 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 62 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 2 optimal weight: 0.4980 chunk 122 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 26 optimal weight: 0.3980 chunk 80 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 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 727 HIS C 115 ASN C 233 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.174662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.147181 restraints weight = 15809.471| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 2.45 r_work: 0.3719 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 10283 Z= 0.273 Angle : 0.629 12.087 13920 Z= 0.316 Chirality : 0.044 0.153 1603 Planarity : 0.004 0.048 1761 Dihedral : 4.317 20.613 1338 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.39 % Allowed : 19.20 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.25), residues: 1237 helix: 1.77 (0.21), residues: 624 sheet: 0.26 (0.38), residues: 199 loop : 0.07 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 490 HIS 0.006 0.001 HIS B 90 PHE 0.027 0.002 PHE A 796 TYR 0.032 0.002 TYR B 73 ARG 0.006 0.000 ARG A 121 *********************** 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 274 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 247 time to evaluate : 1.254 Fit side-chains revert: symmetry clash REVERT: A 201 SER cc_start: 0.8080 (t) cc_final: 0.7780 (t) REVERT: A 416 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7140 (mp0) REVERT: A 419 LYS cc_start: 0.8176 (ttpt) cc_final: 0.7907 (ttmt) REVERT: A 488 GLU cc_start: 0.7885 (tp30) cc_final: 0.7611 (mm-30) REVERT: A 567 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7413 (mp0) REVERT: A 574 ASP cc_start: 0.7545 (OUTLIER) cc_final: 0.7296 (t0) REVERT: A 584 GLU cc_start: 0.7487 (tp30) cc_final: 0.6933 (tm-30) REVERT: A 596 HIS cc_start: 0.8332 (m-70) cc_final: 0.8012 (m170) REVERT: A 630 LYS cc_start: 0.8084 (mttp) cc_final: 0.7809 (mtmm) REVERT: A 637 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8760 (mp) REVERT: A 643 MET cc_start: 0.8359 (mmm) cc_final: 0.8021 (mmt) REVERT: A 659 GLU cc_start: 0.7167 (pp20) cc_final: 0.6538 (tm-30) REVERT: A 663 MET cc_start: 0.8004 (ttm) cc_final: 0.7780 (ttm) REVERT: A 666 ASN cc_start: 0.7460 (t0) cc_final: 0.7158 (t0) REVERT: A 686 ARG cc_start: 0.7253 (tmm160) cc_final: 0.6685 (tmm160) REVERT: A 819 ARG cc_start: 0.7717 (mpp80) cc_final: 0.7461 (mpp80) REVERT: A 868 MET cc_start: 0.7347 (mtm) cc_final: 0.6246 (mtm) REVERT: B 122 LYS cc_start: 0.8125 (tmmt) cc_final: 0.7681 (tmmt) REVERT: C 14 LYS cc_start: 0.8590 (mtmt) cc_final: 0.8355 (mtmt) REVERT: C 67 LYS cc_start: 0.7792 (mtmm) cc_final: 0.7576 (mtmm) REVERT: C 95 PHE cc_start: 0.8229 (m-80) cc_final: 0.7960 (m-80) REVERT: C 176 PHE cc_start: 0.8375 (p90) cc_final: 0.8164 (p90) REVERT: C 269 LYS cc_start: 0.8179 (mtmm) cc_final: 0.7903 (mtmm) outliers start: 27 outliers final: 20 residues processed: 257 average time/residue: 1.2000 time to fit residues: 332.2936 Evaluate side-chains 262 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 240 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 532 HIS Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 652 GLN Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 217 GLU Chi-restraints excluded: chain C residue 277 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 72 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 75 optimal weight: 10.0000 chunk 12 optimal weight: 0.0870 chunk 82 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 104 optimal weight: 0.2980 chunk 63 optimal weight: 0.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 HIS A 727 HIS C 115 ASN C 233 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.175267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.147685 restraints weight = 15971.498| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 2.47 r_work: 0.3724 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10283 Z= 0.238 Angle : 0.627 10.466 13920 Z= 0.313 Chirality : 0.044 0.155 1603 Planarity : 0.004 0.047 1761 Dihedral : 4.266 22.715 1338 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.74 % Allowed : 19.91 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.25), residues: 1237 helix: 1.83 (0.21), residues: 624 sheet: 0.30 (0.38), residues: 199 loop : 0.12 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 490 HIS 0.006 0.001 HIS B 90 PHE 0.021 0.002 PHE A 775 TYR 0.028 0.002 TYR B 73 ARG 0.008 0.000 ARG A 121 *********************** 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 279 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 248 time to evaluate : 1.201 Fit side-chains revert: symmetry clash REVERT: A 201 SER cc_start: 0.8047 (t) cc_final: 0.7744 (t) REVERT: A 416 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7149 (mp0) REVERT: A 419 LYS cc_start: 0.8174 (ttpt) cc_final: 0.7862 (ttmp) REVERT: A 488 GLU cc_start: 0.7897 (tp30) cc_final: 0.7603 (mm-30) REVERT: A 567 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7323 (mp0) REVERT: A 574 ASP cc_start: 0.7549 (t70) cc_final: 0.7299 (t0) REVERT: A 584 GLU cc_start: 0.7439 (tp30) cc_final: 0.6923 (tm-30) REVERT: A 595 LYS cc_start: 0.8718 (tmmm) cc_final: 0.8192 (tppp) REVERT: A 630 LYS cc_start: 0.8010 (mttp) cc_final: 0.7663 (mtmm) REVERT: A 643 MET cc_start: 0.8315 (mmm) cc_final: 0.7974 (mmt) REVERT: A 659 GLU cc_start: 0.7211 (pp20) cc_final: 0.6630 (tm-30) REVERT: A 663 MET cc_start: 0.8011 (ttm) cc_final: 0.7807 (ttm) REVERT: A 666 ASN cc_start: 0.7363 (t0) cc_final: 0.7040 (t0) REVERT: A 684 GLU cc_start: 0.7230 (mt-10) cc_final: 0.6996 (mt-10) REVERT: A 686 ARG cc_start: 0.7266 (tmm160) cc_final: 0.6805 (tmm160) REVERT: A 771 PHE cc_start: 0.8783 (m-80) cc_final: 0.8486 (m-80) REVERT: A 868 MET cc_start: 0.7366 (mtm) cc_final: 0.6262 (mtm) REVERT: B 88 LEU cc_start: 0.7204 (OUTLIER) cc_final: 0.6910 (mp) REVERT: B 122 LYS cc_start: 0.8099 (tmmt) cc_final: 0.7665 (tmmt) REVERT: C 14 LYS cc_start: 0.8557 (mtmt) cc_final: 0.8340 (mtmt) REVERT: C 42 THR cc_start: 0.8331 (m) cc_final: 0.7997 (p) REVERT: C 67 LYS cc_start: 0.7771 (mtmm) cc_final: 0.7544 (mtmm) REVERT: C 95 PHE cc_start: 0.8151 (m-80) cc_final: 0.7743 (m-80) REVERT: C 176 PHE cc_start: 0.8370 (p90) cc_final: 0.8060 (p90) REVERT: C 269 LYS cc_start: 0.8171 (mtmm) cc_final: 0.7899 (mtmm) outliers start: 31 outliers final: 17 residues processed: 262 average time/residue: 1.1358 time to fit residues: 321.7334 Evaluate side-chains 261 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 243 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 532 HIS Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 652 GLN Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 217 GLU Chi-restraints excluded: chain C residue 277 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 52 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 63 optimal weight: 0.0980 chunk 68 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 0 optimal weight: 50.0000 chunk 59 optimal weight: 0.9980 chunk 72 optimal weight: 9.9990 chunk 92 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 727 HIS C 115 ASN C 233 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.174582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.146957 restraints weight = 15963.326| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 2.48 r_work: 0.3709 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 10283 Z= 0.322 Angle : 0.669 15.982 13920 Z= 0.333 Chirality : 0.045 0.167 1603 Planarity : 0.005 0.053 1761 Dihedral : 4.342 21.101 1338 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.65 % Allowed : 20.62 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.24), residues: 1237 helix: 1.64 (0.21), residues: 625 sheet: 0.31 (0.38), residues: 199 loop : 0.10 (0.32), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 490 HIS 0.005 0.001 HIS B 90 PHE 0.025 0.002 PHE C 113 TYR 0.028 0.002 TYR B 73 ARG 0.009 0.000 ARG A 121 *********************** 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 275 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 245 time to evaluate : 1.170 Fit side-chains revert: symmetry clash REVERT: A 201 SER cc_start: 0.8104 (t) cc_final: 0.7803 (t) REVERT: A 248 ARG cc_start: 0.7471 (tpt90) cc_final: 0.7014 (tpt90) REVERT: A 252 MET cc_start: 0.8156 (mtt) cc_final: 0.7539 (mtt) REVERT: A 416 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7179 (mp0) REVERT: A 419 LYS cc_start: 0.8181 (ttpt) cc_final: 0.7867 (ttmp) REVERT: A 488 GLU cc_start: 0.7951 (tp30) cc_final: 0.7656 (mm-30) REVERT: A 567 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7335 (mp0) REVERT: A 574 ASP cc_start: 0.7586 (OUTLIER) cc_final: 0.7340 (t0) REVERT: A 584 GLU cc_start: 0.7501 (tp30) cc_final: 0.6945 (tm-30) REVERT: A 630 LYS cc_start: 0.8121 (mttp) cc_final: 0.7761 (mtmm) REVERT: A 643 MET cc_start: 0.8333 (mmm) cc_final: 0.7981 (mmt) REVERT: A 659 GLU cc_start: 0.7240 (pp20) cc_final: 0.6681 (tm-30) REVERT: A 666 ASN cc_start: 0.7505 (t0) cc_final: 0.7172 (t0) REVERT: A 684 GLU cc_start: 0.7271 (mt-10) cc_final: 0.7014 (mt-10) REVERT: A 686 ARG cc_start: 0.7304 (tmm160) cc_final: 0.7010 (tmm160) REVERT: A 771 PHE cc_start: 0.8846 (m-80) cc_final: 0.8546 (m-80) REVERT: A 800 GLU cc_start: 0.8238 (mm-30) cc_final: 0.8003 (mm-30) REVERT: A 819 ARG cc_start: 0.7517 (mpp80) cc_final: 0.7177 (mpp80) REVERT: A 868 MET cc_start: 0.7397 (mtm) cc_final: 0.6300 (mtm) REVERT: B 89 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.8070 (pp) REVERT: B 122 LYS cc_start: 0.8111 (tmmt) cc_final: 0.7677 (tmmt) REVERT: C 14 LYS cc_start: 0.8549 (mtmt) cc_final: 0.8339 (mtmt) REVERT: C 67 LYS cc_start: 0.7768 (mtmm) cc_final: 0.7556 (mtmm) REVERT: C 95 PHE cc_start: 0.8046 (m-80) cc_final: 0.7686 (m-80) REVERT: C 176 PHE cc_start: 0.8382 (p90) cc_final: 0.8091 (p90) REVERT: C 269 LYS cc_start: 0.8174 (mtmm) cc_final: 0.7909 (mtmm) outliers start: 30 outliers final: 19 residues processed: 256 average time/residue: 1.1810 time to fit residues: 325.3507 Evaluate side-chains 265 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 244 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 532 HIS Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 652 GLN Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 277 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 36 optimal weight: 0.9980 chunk 64 optimal weight: 0.4980 chunk 98 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 51 optimal weight: 0.4980 chunk 60 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 123 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 ASN A 727 HIS C 115 ASN C 233 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.175489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.147876 restraints weight = 15950.539| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 2.49 r_work: 0.3721 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 10283 Z= 0.285 Angle : 0.688 14.845 13920 Z= 0.338 Chirality : 0.045 0.166 1603 Planarity : 0.005 0.048 1761 Dihedral : 4.331 20.767 1338 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.21 % Allowed : 22.21 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.24), residues: 1237 helix: 1.62 (0.21), residues: 625 sheet: 0.28 (0.38), residues: 199 loop : 0.14 (0.32), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 490 HIS 0.005 0.001 HIS B 90 PHE 0.038 0.002 PHE A 640 TYR 0.029 0.002 TYR B 73 ARG 0.010 0.001 ARG A 121 *********************** 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 272 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 247 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 SER cc_start: 0.8066 (t) cc_final: 0.7764 (t) REVERT: A 248 ARG cc_start: 0.7379 (tpt90) cc_final: 0.7174 (tpt90) REVERT: A 416 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7181 (mp0) REVERT: A 419 LYS cc_start: 0.8172 (ttpt) cc_final: 0.7855 (ttmp) REVERT: A 488 GLU cc_start: 0.7951 (tp30) cc_final: 0.7624 (mm-30) REVERT: A 567 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7268 (mp0) REVERT: A 574 ASP cc_start: 0.7569 (OUTLIER) cc_final: 0.7321 (t0) REVERT: A 584 GLU cc_start: 0.7470 (tp30) cc_final: 0.6933 (tm-30) REVERT: A 590 MET cc_start: 0.8368 (mmm) cc_final: 0.7969 (tpt) REVERT: A 591 ASP cc_start: 0.7623 (t70) cc_final: 0.7328 (t0) REVERT: A 595 LYS cc_start: 0.8639 (tmmm) cc_final: 0.8330 (tmmm) REVERT: A 596 HIS cc_start: 0.8310 (m-70) cc_final: 0.7997 (m170) REVERT: A 630 LYS cc_start: 0.8119 (mttp) cc_final: 0.7763 (mtmm) REVERT: A 643 MET cc_start: 0.8317 (mmm) cc_final: 0.7977 (mmt) REVERT: A 659 GLU cc_start: 0.7261 (pp20) cc_final: 0.6858 (tm-30) REVERT: A 661 ARG cc_start: 0.8300 (tmm-80) cc_final: 0.7799 (ttt-90) REVERT: A 666 ASN cc_start: 0.7472 (t0) cc_final: 0.7124 (t0) REVERT: A 686 ARG cc_start: 0.7324 (tmm160) cc_final: 0.7022 (tmm160) REVERT: A 771 PHE cc_start: 0.8858 (m-80) cc_final: 0.8478 (m-80) REVERT: A 800 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7934 (mm-30) REVERT: A 819 ARG cc_start: 0.7522 (mpp80) cc_final: 0.7231 (mpp80) REVERT: A 868 MET cc_start: 0.7388 (mtm) cc_final: 0.6296 (mtm) REVERT: B 89 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.8024 (pp) REVERT: B 122 LYS cc_start: 0.8097 (tmmt) cc_final: 0.7676 (tmmt) REVERT: C 14 LYS cc_start: 0.8548 (mtmt) cc_final: 0.8345 (mtmt) REVERT: C 67 LYS cc_start: 0.7775 (mtmm) cc_final: 0.7557 (mtmm) REVERT: C 95 PHE cc_start: 0.7881 (m-80) cc_final: 0.7495 (m-80) REVERT: C 176 PHE cc_start: 0.8367 (p90) cc_final: 0.8034 (p90) REVERT: C 269 LYS cc_start: 0.8182 (mtmm) cc_final: 0.7910 (mtmm) outliers start: 25 outliers final: 20 residues processed: 256 average time/residue: 1.2463 time to fit residues: 344.1643 Evaluate side-chains 265 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 243 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 532 HIS Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 652 GLN Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 217 GLU Chi-restraints excluded: chain C residue 277 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 56 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 114 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 72 optimal weight: 50.0000 chunk 124 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 82 optimal weight: 0.3980 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 400 GLN A 727 HIS C 115 ASN C 233 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.175634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.147865 restraints weight = 15942.975| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 2.49 r_work: 0.3729 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 10283 Z= 0.286 Angle : 0.695 14.573 13920 Z= 0.343 Chirality : 0.045 0.198 1603 Planarity : 0.005 0.048 1761 Dihedral : 4.331 18.897 1338 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.48 % Allowed : 22.30 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.24), residues: 1237 helix: 1.60 (0.21), residues: 625 sheet: 0.28 (0.38), residues: 199 loop : 0.12 (0.32), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 490 HIS 0.006 0.001 HIS B 90 PHE 0.036 0.002 PHE C 113 TYR 0.024 0.002 TYR B 73 ARG 0.009 0.000 ARG A 121 ********************** 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 268 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 240 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 SER cc_start: 0.8067 (t) cc_final: 0.7766 (t) REVERT: A 416 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7180 (mp0) REVERT: A 419 LYS cc_start: 0.8183 (ttpt) cc_final: 0.7865 (ttmp) REVERT: A 488 GLU cc_start: 0.7939 (tp30) cc_final: 0.7626 (mm-30) REVERT: A 567 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7260 (mp0) REVERT: A 574 ASP cc_start: 0.7511 (OUTLIER) cc_final: 0.7263 (t0) REVERT: A 584 GLU cc_start: 0.7445 (tp30) cc_final: 0.6924 (tm-30) REVERT: A 590 MET cc_start: 0.8353 (mmm) cc_final: 0.7952 (tpt) REVERT: A 591 ASP cc_start: 0.7608 (t70) cc_final: 0.7326 (t0) REVERT: A 630 LYS cc_start: 0.8126 (mttp) cc_final: 0.7862 (mtmm) REVERT: A 643 MET cc_start: 0.8322 (mmm) cc_final: 0.7978 (mmt) REVERT: A 659 GLU cc_start: 0.7261 (pp20) cc_final: 0.6851 (tm-30) REVERT: A 661 ARG cc_start: 0.8305 (tmm-80) cc_final: 0.7780 (ttt-90) REVERT: A 666 ASN cc_start: 0.7424 (t0) cc_final: 0.7079 (t0) REVERT: A 771 PHE cc_start: 0.8870 (m-80) cc_final: 0.8442 (m-80) REVERT: A 800 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7894 (mp0) REVERT: A 819 ARG cc_start: 0.7679 (mpp80) cc_final: 0.7474 (mpp80) REVERT: A 868 MET cc_start: 0.7390 (mtm) cc_final: 0.6313 (mtm) REVERT: B 88 LEU cc_start: 0.7190 (OUTLIER) cc_final: 0.6898 (mp) REVERT: B 89 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.8022 (pp) REVERT: B 122 LYS cc_start: 0.8099 (tmmt) cc_final: 0.7682 (tmmt) REVERT: C 67 LYS cc_start: 0.7761 (mtmm) cc_final: 0.7542 (mtmm) REVERT: C 95 PHE cc_start: 0.7827 (m-80) cc_final: 0.7502 (m-80) REVERT: C 269 LYS cc_start: 0.8177 (mtmm) cc_final: 0.7907 (mtmm) outliers start: 28 outliers final: 22 residues processed: 248 average time/residue: 1.2113 time to fit residues: 323.5502 Evaluate side-chains 265 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 240 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 532 HIS Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 652 GLN Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 217 GLU Chi-restraints excluded: chain C residue 277 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 114 optimal weight: 0.0980 chunk 109 optimal weight: 0.7980 chunk 72 optimal weight: 30.0000 chunk 26 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 121 optimal weight: 0.0980 chunk 33 optimal weight: 0.9990 chunk 81 optimal weight: 0.4980 chunk 49 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 35 optimal weight: 0.3980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 HIS A 727 HIS C 115 ASN C 233 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.176397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.148677 restraints weight = 15941.692| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 2.49 r_work: 0.3746 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 10283 Z= 0.245 Angle : 0.698 14.574 13920 Z= 0.342 Chirality : 0.044 0.162 1603 Planarity : 0.005 0.049 1761 Dihedral : 4.266 17.600 1338 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.48 % Allowed : 22.39 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.24), residues: 1237 helix: 1.60 (0.21), residues: 629 sheet: 0.29 (0.39), residues: 199 loop : 0.10 (0.32), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 490 HIS 0.006 0.001 HIS B 90 PHE 0.031 0.002 PHE A 640 TYR 0.021 0.001 TYR B 73 ARG 0.011 0.001 ARG A 248 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7594.21 seconds wall clock time: 134 minutes 48.14 seconds (8088.14 seconds total)