Starting phenix.real_space_refine on Sat Nov 16 01:08:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syo_40886/11_2024/8syo_40886.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syo_40886/11_2024/8syo_40886.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syo_40886/11_2024/8syo_40886.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syo_40886/11_2024/8syo_40886.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syo_40886/11_2024/8syo_40886.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syo_40886/11_2024/8syo_40886.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= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 6487 2.51 5 N 1695 2.21 5 O 1825 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 6.32, per 1000 atoms: 0.63 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: 2.73 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: 1.37 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: 3.85 Time building geometry restraints manager: 2.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3228 1.34 - 1.46: 1988 1.46 - 1.58: 4977 1.58 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 10283 Sorted by residual: bond pdb=" CG1 ILE A 712 " pdb=" CD1 ILE A 712 " ideal model delta sigma weight residual 1.513 1.444 0.069 3.90e-02 6.57e+02 3.11e+00 bond pdb=" CA ILE A 712 " pdb=" CB ILE A 712 " ideal model delta sigma weight residual 1.539 1.547 -0.008 5.40e-03 3.43e+04 2.09e+00 bond pdb=" N ILE A 712 " pdb=" CA ILE A 712 " ideal model delta sigma weight residual 1.463 1.478 -0.015 1.20e-02 6.94e+03 1.55e+00 bond pdb=" C THR A 534 " pdb=" N PRO A 535 " ideal model delta sigma weight residual 1.334 1.361 -0.027 2.34e-02 1.83e+03 1.36e+00 bond pdb=" SD MET A 395 " pdb=" CE MET A 395 " ideal model delta sigma weight residual 1.791 1.762 0.029 2.50e-02 1.60e+03 1.34e+00 ... (remaining 10278 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 13658 1.95 - 3.90: 222 3.90 - 5.85: 34 5.85 - 7.80: 4 7.80 - 9.75: 2 Bond angle restraints: 13920 Sorted by residual: angle pdb=" N ILE A 712 " pdb=" CA ILE A 712 " pdb=" CB ILE A 712 " ideal model delta sigma weight residual 110.45 115.92 -5.47 7.80e-01 1.64e+00 4.91e+01 angle pdb=" C ILE A 712 " pdb=" CA ILE A 712 " pdb=" CB ILE A 712 " ideal model delta sigma weight residual 114.00 106.87 7.13 1.31e+00 5.83e-01 2.96e+01 angle pdb=" C LEU B 44 " pdb=" N CYS B 45 " pdb=" CA CYS B 45 " ideal model delta sigma weight residual 121.54 129.09 -7.55 1.91e+00 2.74e-01 1.56e+01 angle pdb=" CB LYS A 602 " pdb=" CG LYS A 602 " pdb=" CD LYS A 602 " ideal model delta sigma weight residual 111.30 103.21 8.09 2.30e+00 1.89e-01 1.24e+01 angle pdb=" CB MET A 533 " pdb=" CG MET A 533 " pdb=" SD MET A 533 " ideal model delta sigma weight residual 112.70 102.95 9.75 3.00e+00 1.11e-01 1.06e+01 ... (remaining 13915 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 5653 17.65 - 35.31: 473 35.31 - 52.96: 67 52.96 - 70.61: 8 70.61 - 88.27: 9 Dihedral angle restraints: 6210 sinusoidal: 2513 harmonic: 3697 Sorted by residual: dihedral pdb=" CA CYS A 737 " pdb=" C CYS A 737 " pdb=" N LEU A 738 " pdb=" CA LEU A 738 " ideal model delta harmonic sigma weight residual -180.00 -161.24 -18.76 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA GLY C 148 " pdb=" C GLY C 148 " pdb=" N LYS C 149 " pdb=" CA LYS C 149 " ideal model delta harmonic sigma weight residual 180.00 161.28 18.72 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA PRO A 535 " pdb=" C PRO A 535 " pdb=" N ASP A 536 " pdb=" CA ASP A 536 " ideal model delta harmonic sigma weight residual -180.00 -162.34 -17.66 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 6207 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1131 0.040 - 0.080: 318 0.080 - 0.120: 130 0.120 - 0.160: 23 0.160 - 0.199: 1 Chirality restraints: 1603 Sorted by residual: chirality pdb=" CB ILE A 718 " pdb=" CA ILE A 718 " pdb=" CG1 ILE A 718 " pdb=" CG2 ILE A 718 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.95e-01 chirality pdb=" CA MET A 533 " pdb=" N MET A 533 " pdb=" C MET A 533 " pdb=" CB MET A 533 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.82e-01 chirality pdb=" CA PRO A 535 " pdb=" N PRO A 535 " pdb=" C PRO A 535 " pdb=" CB PRO A 535 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.75e-01 ... (remaining 1600 not shown) Planarity restraints: 1761 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 384 " -0.055 5.00e-02 4.00e+02 8.35e-02 1.11e+01 pdb=" N PRO A 385 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO A 385 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 385 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 821 " -0.019 2.00e-02 2.50e+03 1.65e-02 5.45e+00 pdb=" CG TYR A 821 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR A 821 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A 821 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 821 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 821 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR A 821 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 821 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 534 " -0.032 5.00e-02 4.00e+02 4.83e-02 3.74e+00 pdb=" N PRO A 535 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 535 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 535 " -0.027 5.00e-02 4.00e+02 ... (remaining 1758 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 453 2.73 - 3.27: 10483 3.27 - 3.81: 16677 3.81 - 4.36: 19664 4.36 - 4.90: 33992 Nonbonded interactions: 81269 Sorted by model distance: nonbonded pdb=" NZ LYS B 25 " pdb=" O ASP B 174 " model vdw 2.182 3.120 nonbonded pdb=" OH TYR A 387 " pdb=" OH TYR A 391 " model vdw 2.211 3.040 nonbonded pdb=" OE2 GLU A 297 " pdb=" NH2 ARG A 318 " model vdw 2.215 3.120 nonbonded pdb=" O PRO A 34 " pdb=" NZ LYS B 34 " model vdw 2.217 3.120 nonbonded pdb=" O PHE A 656 " pdb=" OG SER A 660 " model vdw 2.232 3.040 ... (remaining 81264 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 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: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 26.200 Find NCS groups from input model: 0.100 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:13.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 10283 Z= 0.253 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 352 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 ASP cc_start: 0.6920 (m-30) cc_final: 0.6653 (m-30) REVERT: A 123 GLU cc_start: 0.7404 (mp0) cc_final: 0.6884 (mp0) REVERT: A 344 MET cc_start: 0.8537 (mmt) cc_final: 0.8164 (mpp) REVERT: A 345 GLU cc_start: 0.7234 (pp20) cc_final: 0.6761 (pp20) REVERT: A 376 GLN cc_start: 0.6893 (tt0) cc_final: 0.6669 (mt0) REVERT: A 408 GLU cc_start: 0.7506 (tt0) cc_final: 0.6837 (tm-30) REVERT: A 416 GLU cc_start: 0.7041 (mp0) cc_final: 0.6501 (mp0) REVERT: A 420 LYS cc_start: 0.8060 (mtpp) cc_final: 0.7784 (mtpm) REVERT: A 488 GLU cc_start: 0.7844 (tp30) cc_final: 0.7200 (tm-30) REVERT: A 567 GLU cc_start: 0.7564 (mp0) cc_final: 0.6937 (mp0) REVERT: A 590 MET cc_start: 0.8216 (mmm) cc_final: 0.8012 (mmm) REVERT: A 591 ASP cc_start: 0.7362 (m-30) cc_final: 0.7150 (m-30) REVERT: A 599 GLU cc_start: 0.7649 (pm20) cc_final: 0.7393 (pp20) REVERT: A 615 LYS cc_start: 0.8094 (tppt) cc_final: 0.7671 (tptp) REVERT: A 626 LEU cc_start: 0.8081 (tp) cc_final: 0.7878 (tt) REVERT: A 652 GLN cc_start: 0.7667 (tp-100) cc_final: 0.7017 (tp-100) REVERT: A 655 SER cc_start: 0.8290 (m) cc_final: 0.7758 (p) REVERT: A 724 LEU cc_start: 0.8033 (mt) cc_final: 0.7798 (mt) REVERT: A 761 ILE cc_start: 0.8516 (mt) cc_final: 0.8112 (mt) REVERT: A 860 ASN cc_start: 0.7812 (t0) cc_final: 0.7554 (t0) REVERT: A 864 CYS cc_start: 0.7524 (m) cc_final: 0.7292 (m) REVERT: A 903 ASP cc_start: 0.7230 (t0) cc_final: 0.7021 (t0) REVERT: B 124 GLU cc_start: 0.7043 (mt-10) cc_final: 0.6598 (tt0) REVERT: B 165 VAL cc_start: 0.8022 (m) cc_final: 0.7549 (p) REVERT: C 20 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8285 (mt-10) REVERT: C 21 VAL cc_start: 0.8634 (t) cc_final: 0.8317 (p) REVERT: C 43 MET cc_start: 0.8870 (tmm) cc_final: 0.8319 (ttp) REVERT: C 50 GLN cc_start: 0.8293 (mm-40) cc_final: 0.7966 (mm-40) REVERT: C 112 VAL cc_start: 0.8775 (p) cc_final: 0.8536 (t) REVERT: C 113 PHE cc_start: 0.8487 (m-10) cc_final: 0.8191 (m-10) REVERT: C 175 LYS cc_start: 0.8177 (mppt) cc_final: 0.7931 (mppt) REVERT: C 200 GLU cc_start: 0.7407 (mt-10) cc_final: 0.7166 (mt-10) REVERT: C 201 SER cc_start: 0.8473 (p) cc_final: 0.8247 (m) REVERT: C 231 GLU cc_start: 0.7537 (pt0) cc_final: 0.7240 (pt0) outliers start: 0 outliers final: 0 residues processed: 352 average time/residue: 1.2383 time to fit residues: 468.8085 Evaluate side-chains 283 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 1.196 ------------------------------------------------------------------------------- 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: 0.0060 chunk 94 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 63 optimal weight: 0.4980 chunk 50 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 113 optimal weight: 0.5980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 ASN A 673 GLN ** A 792 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 4 HIS B 72 ASN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 HIS C 115 ASN C 117 GLN C 183 ASN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10283 Z= 0.240 Angle : 0.624 10.373 13920 Z= 0.319 Chirality : 0.045 0.198 1603 Planarity : 0.005 0.061 1761 Dihedral : 4.249 19.268 1338 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.63 % Allowed : 13.81 % Favored : 82.57 % 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: 1.20 (0.25), residues: 1237 helix: 1.47 (0.21), residues: 623 sheet: 0.57 (0.39), residues: 195 loop : 0.02 (0.32), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 490 HIS 0.013 0.001 HIS A 789 PHE 0.025 0.002 PHE A 796 TYR 0.031 0.002 TYR B 73 ARG 0.007 0.001 ARG A 766 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 290 time to evaluate : 1.194 Fit side-chains REVERT: A 123 GLU cc_start: 0.7287 (mp0) cc_final: 0.6704 (mp0) REVERT: A 344 MET cc_start: 0.8595 (mmt) cc_final: 0.8177 (mpp) REVERT: A 345 GLU cc_start: 0.7186 (pp20) cc_final: 0.6673 (pp20) REVERT: A 366 LYS cc_start: 0.8325 (ptpp) cc_final: 0.7999 (tppt) REVERT: A 395 MET cc_start: 0.7907 (mtt) cc_final: 0.7652 (mtp) REVERT: A 416 GLU cc_start: 0.6942 (mp0) cc_final: 0.6485 (mp0) REVERT: A 419 LYS cc_start: 0.7991 (ttpt) cc_final: 0.7788 (ttpp) REVERT: A 420 LYS cc_start: 0.8008 (mtpp) cc_final: 0.7697 (mtpm) REVERT: A 567 GLU cc_start: 0.7728 (mp0) cc_final: 0.7196 (mp0) REVERT: A 591 ASP cc_start: 0.7342 (m-30) cc_final: 0.7113 (m-30) REVERT: A 599 GLU cc_start: 0.7686 (pm20) cc_final: 0.7419 (pp20) REVERT: A 615 LYS cc_start: 0.7955 (tppt) cc_final: 0.7586 (tptp) REVERT: A 652 GLN cc_start: 0.7717 (tp-100) cc_final: 0.6654 (tp-100) REVERT: A 655 SER cc_start: 0.8119 (m) cc_final: 0.7784 (p) REVERT: A 870 GLN cc_start: 0.7998 (mm-40) cc_final: 0.7479 (mm-40) REVERT: A 903 ASP cc_start: 0.7224 (t0) cc_final: 0.7019 (t0) REVERT: B 108 ARG cc_start: 0.7168 (mtm-85) cc_final: 0.6892 (mtm-85) REVERT: B 143 TYR cc_start: 0.8433 (p90) cc_final: 0.8229 (p90) REVERT: C 21 VAL cc_start: 0.8605 (t) cc_final: 0.8294 (p) REVERT: C 50 GLN cc_start: 0.8267 (mm-40) cc_final: 0.7939 (mm-40) REVERT: C 95 PHE cc_start: 0.8636 (m-80) cc_final: 0.8408 (m-80) REVERT: C 112 VAL cc_start: 0.8799 (p) cc_final: 0.8500 (t) REVERT: C 113 PHE cc_start: 0.8507 (m-10) cc_final: 0.8224 (m-10) REVERT: C 173 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8552 (mp) REVERT: C 231 GLU cc_start: 0.7485 (pt0) cc_final: 0.7179 (pt0) outliers start: 41 outliers final: 11 residues processed: 308 average time/residue: 1.2809 time to fit residues: 422.4345 Evaluate side-chains 254 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 242 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain B residue 4 HIS Chi-restraints excluded: chain B residue 43 ASN Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 173 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 0.3980 chunk 35 optimal weight: 0.0030 chunk 94 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 112 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 91 optimal weight: 0.9980 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 GLN A 380 GLN ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 HIS A 666 ASN ** A 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 792 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 806 GLN A 826 HIS ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 GLN C 115 ASN C 183 ASN C 233 GLN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10283 Z= 0.234 Angle : 0.641 12.706 13920 Z= 0.321 Chirality : 0.044 0.269 1603 Planarity : 0.004 0.050 1761 Dihedral : 4.284 19.498 1338 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.72 % Allowed : 18.41 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.32 (0.25), residues: 1237 helix: 1.60 (0.21), residues: 625 sheet: 0.60 (0.39), residues: 192 loop : 0.03 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 6 HIS 0.008 0.001 HIS B 128 PHE 0.030 0.002 PHE A 358 TYR 0.027 0.001 TYR B 73 ARG 0.009 0.001 ARG C 126 *********************** 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 300 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 258 time to evaluate : 1.245 Fit side-chains REVERT: A 22 LEU cc_start: 0.6384 (pp) cc_final: 0.6063 (mt) REVERT: A 366 LYS cc_start: 0.8357 (ptpp) cc_final: 0.7995 (tppt) REVERT: A 419 LYS cc_start: 0.8007 (ttpt) cc_final: 0.7797 (ttpp) REVERT: A 561 SER cc_start: 0.8579 (m) cc_final: 0.8201 (t) REVERT: A 591 ASP cc_start: 0.7386 (m-30) cc_final: 0.7156 (m-30) REVERT: A 595 LYS cc_start: 0.8447 (tmmt) cc_final: 0.8197 (tttm) REVERT: A 599 GLU cc_start: 0.7654 (pm20) cc_final: 0.7425 (pp20) REVERT: A 615 LYS cc_start: 0.7990 (tppt) cc_final: 0.7610 (tptp) REVERT: A 643 MET cc_start: 0.8418 (mmm) cc_final: 0.8110 (mmm) REVERT: A 652 GLN cc_start: 0.7663 (tp-100) cc_final: 0.6636 (tp-100) REVERT: A 655 SER cc_start: 0.8085 (m) cc_final: 0.7752 (p) REVERT: A 689 MET cc_start: 0.7727 (mtp) cc_final: 0.7482 (ttm) REVERT: A 836 TYR cc_start: 0.7696 (m-10) cc_final: 0.7479 (m-10) REVERT: A 870 GLN cc_start: 0.7505 (mm-40) cc_final: 0.6795 (tm-30) REVERT: A 873 GLU cc_start: 0.7181 (tm-30) cc_final: 0.6958 (pp20) REVERT: B 165 VAL cc_start: 0.7929 (OUTLIER) cc_final: 0.7591 (m) REVERT: C 43 MET cc_start: 0.8779 (tmm) cc_final: 0.8523 (ttp) REVERT: C 50 GLN cc_start: 0.8280 (mm-40) cc_final: 0.7950 (mm-40) REVERT: C 112 VAL cc_start: 0.8850 (p) cc_final: 0.8572 (t) REVERT: C 175 LYS cc_start: 0.8204 (mppt) cc_final: 0.7930 (mppt) REVERT: C 231 GLU cc_start: 0.7534 (pt0) cc_final: 0.7220 (pt0) outliers start: 42 outliers final: 9 residues processed: 277 average time/residue: 1.2339 time to fit residues: 367.8873 Evaluate side-chains 255 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 245 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 151 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 0.0970 chunk 85 optimal weight: 0.8980 chunk 59 optimal weight: 0.0060 chunk 12 optimal weight: 0.9980 chunk 54 optimal weight: 0.0050 chunk 76 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 chunk 100 optimal weight: 2.9990 overall best weight: 0.3008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 376 GLN A 471 ASN ** A 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 ASN ** A 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 792 HIS A 826 HIS B 4 HIS ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN C 183 ASN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10283 Z= 0.199 Angle : 0.614 12.438 13920 Z= 0.309 Chirality : 0.043 0.157 1603 Planarity : 0.004 0.046 1761 Dihedral : 4.212 18.566 1338 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.36 % Allowed : 21.42 % 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: 1.48 (0.25), residues: 1237 helix: 1.77 (0.21), residues: 626 sheet: 0.70 (0.39), residues: 192 loop : 0.03 (0.32), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 6 HIS 0.006 0.001 HIS B 128 PHE 0.018 0.001 PHE A 796 TYR 0.025 0.001 TYR B 73 ARG 0.008 0.001 ARG A 819 *********************** 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 287 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 249 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 288 ARG cc_start: 0.8097 (ttt180) cc_final: 0.7818 (ttt-90) REVERT: A 416 GLU cc_start: 0.7182 (mm-30) cc_final: 0.6672 (mp0) REVERT: A 419 LYS cc_start: 0.7978 (ttpt) cc_final: 0.7749 (ttpp) REVERT: A 561 SER cc_start: 0.8608 (m) cc_final: 0.8213 (t) REVERT: A 591 ASP cc_start: 0.7350 (m-30) cc_final: 0.7113 (m-30) REVERT: A 595 LYS cc_start: 0.8495 (tmmt) cc_final: 0.8107 (tmmt) REVERT: A 615 LYS cc_start: 0.7990 (tppt) cc_final: 0.7608 (tptp) REVERT: A 643 MET cc_start: 0.8439 (mmm) cc_final: 0.8106 (mmm) REVERT: A 652 GLN cc_start: 0.7638 (tp-100) cc_final: 0.6617 (tp-100) REVERT: A 655 SER cc_start: 0.7985 (m) cc_final: 0.7683 (p) REVERT: A 806 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.8026 (mm110) REVERT: A 811 GLU cc_start: 0.6367 (tm-30) cc_final: 0.6068 (tp30) REVERT: A 870 GLN cc_start: 0.7421 (mm-40) cc_final: 0.7151 (mm-40) REVERT: B 143 TYR cc_start: 0.8395 (p90) cc_final: 0.7891 (p90) REVERT: B 165 VAL cc_start: 0.7903 (OUTLIER) cc_final: 0.7515 (m) REVERT: C 13 ASN cc_start: 0.8629 (p0) cc_final: 0.8401 (p0) REVERT: C 43 MET cc_start: 0.8754 (tmm) cc_final: 0.8465 (ttp) REVERT: C 50 GLN cc_start: 0.8307 (mm-40) cc_final: 0.7956 (mm-40) REVERT: C 79 VAL cc_start: 0.9005 (t) cc_final: 0.8538 (m) REVERT: C 175 LYS cc_start: 0.8247 (mppt) cc_final: 0.7968 (mppt) REVERT: C 231 GLU cc_start: 0.7525 (pt0) cc_final: 0.7222 (pt0) outliers start: 38 outliers final: 14 residues processed: 269 average time/residue: 1.2902 time to fit residues: 371.6814 Evaluate side-chains 249 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 233 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 806 GLN Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 102 ASN Chi-restraints excluded: chain C residue 151 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 68 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 103 optimal weight: 0.0970 chunk 83 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 108 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 GLN A 666 ASN ** A 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 HIS ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 GLN C 115 ASN C 183 ASN C 233 GLN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10283 Z= 0.269 Angle : 0.639 11.653 13920 Z= 0.321 Chirality : 0.044 0.203 1603 Planarity : 0.004 0.046 1761 Dihedral : 4.302 19.021 1338 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.25 % Allowed : 22.48 % Favored : 73.27 % 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: 1.42 (0.25), residues: 1237 helix: 1.64 (0.21), residues: 631 sheet: 0.74 (0.39), residues: 196 loop : 0.05 (0.33), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 6 HIS 0.006 0.001 HIS B 128 PHE 0.033 0.002 PHE A 358 TYR 0.028 0.001 TYR B 73 ARG 0.009 0.000 ARG A 819 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 257 time to evaluate : 1.128 Fit side-chains REVERT: A 123 GLU cc_start: 0.7356 (mp0) cc_final: 0.6913 (mt-10) REVERT: A 288 ARG cc_start: 0.8124 (ttt180) cc_final: 0.7824 (ttt-90) REVERT: A 561 SER cc_start: 0.8621 (m) cc_final: 0.8211 (t) REVERT: A 591 ASP cc_start: 0.7386 (m-30) cc_final: 0.7151 (m-30) REVERT: A 595 LYS cc_start: 0.8478 (tmmt) cc_final: 0.8234 (tmmt) REVERT: A 615 LYS cc_start: 0.8034 (tppt) cc_final: 0.7612 (tptp) REVERT: A 643 MET cc_start: 0.8498 (mmm) cc_final: 0.8150 (mmm) REVERT: A 655 SER cc_start: 0.8019 (m) cc_final: 0.7811 (p) REVERT: A 663 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.7773 (tmm) REVERT: A 689 MET cc_start: 0.7777 (mtp) cc_final: 0.7572 (ttm) REVERT: A 754 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7435 (tm-30) REVERT: A 766 ARG cc_start: 0.7547 (tpp80) cc_final: 0.7123 (mtm180) REVERT: A 806 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7917 (mm110) REVERT: A 811 GLU cc_start: 0.6365 (tm-30) cc_final: 0.6025 (tp30) REVERT: A 870 GLN cc_start: 0.7535 (mm-40) cc_final: 0.7025 (mm-40) REVERT: A 873 GLU cc_start: 0.7190 (tm-30) cc_final: 0.6840 (pp20) REVERT: B 143 TYR cc_start: 0.8508 (p90) cc_final: 0.7926 (p90) REVERT: B 165 VAL cc_start: 0.7912 (OUTLIER) cc_final: 0.7498 (m) REVERT: B 168 VAL cc_start: 0.8538 (p) cc_final: 0.8330 (m) REVERT: C 13 ASN cc_start: 0.8655 (p0) cc_final: 0.8383 (p0) REVERT: C 43 MET cc_start: 0.8754 (tmm) cc_final: 0.8507 (ttp) REVERT: C 50 GLN cc_start: 0.8341 (mm-40) cc_final: 0.7937 (mm-40) REVERT: C 66 VAL cc_start: 0.8350 (m) cc_final: 0.8068 (p) REVERT: C 79 VAL cc_start: 0.9050 (t) cc_final: 0.8631 (m) REVERT: C 112 VAL cc_start: 0.8894 (p) cc_final: 0.8599 (t) REVERT: C 175 LYS cc_start: 0.8266 (mppt) cc_final: 0.7973 (mppt) REVERT: C 231 GLU cc_start: 0.7549 (pt0) cc_final: 0.7256 (pt0) outliers start: 48 outliers final: 19 residues processed: 281 average time/residue: 1.2888 time to fit residues: 389.0480 Evaluate side-chains 271 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 248 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain A residue 806 GLN Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 847 ASP Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 173 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 116 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 GLN A 516 HIS ** A 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 HIS B 92 HIS ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 GLN C 115 ASN C 183 ASN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10283 Z= 0.317 Angle : 0.663 12.392 13920 Z= 0.335 Chirality : 0.045 0.163 1603 Planarity : 0.005 0.045 1761 Dihedral : 4.415 19.376 1338 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.45 % Allowed : 24.78 % Favored : 71.77 % 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: 1.25 (0.24), residues: 1237 helix: 1.56 (0.21), residues: 630 sheet: 0.76 (0.40), residues: 183 loop : -0.15 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 6 HIS 0.004 0.001 HIS A 462 PHE 0.024 0.002 PHE A 796 TYR 0.015 0.002 TYR B 73 ARG 0.014 0.001 ARG A 819 *********************** 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 291 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 252 time to evaluate : 1.219 Fit side-chains REVERT: A 123 GLU cc_start: 0.7371 (mp0) cc_final: 0.6937 (mt-10) REVERT: A 416 GLU cc_start: 0.7241 (mm-30) cc_final: 0.6640 (mp0) REVERT: A 561 SER cc_start: 0.8656 (m) cc_final: 0.8214 (t) REVERT: A 567 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7549 (mm-30) REVERT: A 591 ASP cc_start: 0.7418 (m-30) cc_final: 0.7177 (m-30) REVERT: A 595 LYS cc_start: 0.8480 (tmmt) cc_final: 0.8148 (tmmt) REVERT: A 615 LYS cc_start: 0.8031 (tppt) cc_final: 0.7604 (tptp) REVERT: A 663 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7794 (tmm) REVERT: A 754 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7141 (tm-30) REVERT: A 766 ARG cc_start: 0.7444 (tpp80) cc_final: 0.7072 (ttm170) REVERT: A 811 GLU cc_start: 0.6389 (tm-30) cc_final: 0.6005 (tp30) REVERT: A 870 GLN cc_start: 0.7482 (mm-40) cc_final: 0.7016 (mm-40) REVERT: A 873 GLU cc_start: 0.7149 (tm-30) cc_final: 0.6751 (pp20) REVERT: B 143 TYR cc_start: 0.8524 (p90) cc_final: 0.8122 (p90) REVERT: B 168 VAL cc_start: 0.8532 (p) cc_final: 0.8313 (m) REVERT: C 66 VAL cc_start: 0.8376 (m) cc_final: 0.8094 (p) REVERT: C 79 VAL cc_start: 0.9019 (t) cc_final: 0.8662 (m) REVERT: C 112 VAL cc_start: 0.8912 (p) cc_final: 0.8668 (t) outliers start: 39 outliers final: 16 residues processed: 273 average time/residue: 1.3146 time to fit residues: 383.7226 Evaluate side-chains 258 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 240 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 173 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 13 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 88 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 67 optimal weight: 0.4980 chunk 120 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 chunk 74 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 376 GLN A 652 GLN A 666 ASN ** A 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 HIS B 36 GLN ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 ASN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10283 Z= 0.290 Angle : 0.679 10.227 13920 Z= 0.342 Chirality : 0.045 0.159 1603 Planarity : 0.004 0.044 1761 Dihedral : 4.429 19.322 1338 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.72 % Allowed : 26.11 % Favored : 70.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.19 (0.24), residues: 1237 helix: 1.51 (0.21), residues: 629 sheet: 0.54 (0.38), residues: 203 loop : -0.10 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 6 HIS 0.005 0.001 HIS B 90 PHE 0.038 0.002 PHE A 744 TYR 0.014 0.001 TYR B 73 ARG 0.008 0.001 ARG A 819 *********************** 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 292 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 250 time to evaluate : 1.330 Fit side-chains REVERT: A 123 GLU cc_start: 0.7375 (mp0) cc_final: 0.6952 (mt-10) REVERT: A 202 ASP cc_start: 0.7814 (OUTLIER) cc_final: 0.7546 (t70) REVERT: A 416 GLU cc_start: 0.7249 (mm-30) cc_final: 0.6715 (mp0) REVERT: A 561 SER cc_start: 0.8648 (m) cc_final: 0.8202 (t) REVERT: A 567 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7504 (mm-30) REVERT: A 591 ASP cc_start: 0.7403 (m-30) cc_final: 0.7155 (m-30) REVERT: A 595 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.8144 (tmmt) REVERT: A 615 LYS cc_start: 0.8014 (tppt) cc_final: 0.7592 (tptp) REVERT: A 663 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.7802 (tmm) REVERT: A 695 ARG cc_start: 0.7780 (mmm-85) cc_final: 0.7562 (mmm-85) REVERT: A 754 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7101 (tm-30) REVERT: A 811 GLU cc_start: 0.6432 (tm-30) cc_final: 0.6067 (tp30) REVERT: A 855 LYS cc_start: 0.7962 (mtpt) cc_final: 0.7404 (mppt) REVERT: A 870 GLN cc_start: 0.7487 (mm-40) cc_final: 0.7056 (mm-40) REVERT: A 873 GLU cc_start: 0.7131 (tm-30) cc_final: 0.6805 (pp20) REVERT: B 143 TYR cc_start: 0.8486 (p90) cc_final: 0.8085 (p90) REVERT: C 13 ASN cc_start: 0.8665 (p0) cc_final: 0.8392 (p0) REVERT: C 79 VAL cc_start: 0.9036 (t) cc_final: 0.8687 (m) REVERT: C 112 VAL cc_start: 0.8906 (p) cc_final: 0.8687 (t) outliers start: 42 outliers final: 16 residues processed: 269 average time/residue: 1.2984 time to fit residues: 374.0368 Evaluate side-chains 267 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 247 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 532 HIS Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 147 LYS Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 173 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 0.7980 chunk 36 optimal weight: 0.2980 chunk 23 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 59 optimal weight: 0.4980 chunk 11 optimal weight: 0.0010 chunk 94 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN A 376 GLN A 673 GLN ** A 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 806 GLN A 826 HIS ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 ASN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10283 Z= 0.237 Angle : 0.679 13.913 13920 Z= 0.337 Chirality : 0.044 0.185 1603 Planarity : 0.005 0.043 1761 Dihedral : 4.397 19.355 1338 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.45 % Allowed : 27.17 % Favored : 69.38 % 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: 1.61 (0.21), residues: 630 sheet: 0.70 (0.38), residues: 193 loop : -0.12 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 490 HIS 0.005 0.001 HIS B 90 PHE 0.020 0.001 PHE A 775 TYR 0.013 0.001 TYR A 128 ARG 0.009 0.001 ARG A 631 *********************** 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 294 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 255 time to evaluate : 1.219 Fit side-chains revert: symmetry clash REVERT: A 202 ASP cc_start: 0.7707 (OUTLIER) cc_final: 0.7444 (t70) REVERT: A 345 GLU cc_start: 0.7296 (pp20) cc_final: 0.6843 (pp20) REVERT: A 416 GLU cc_start: 0.7207 (mm-30) cc_final: 0.6686 (mp0) REVERT: A 561 SER cc_start: 0.8635 (m) cc_final: 0.8181 (t) REVERT: A 591 ASP cc_start: 0.7376 (m-30) cc_final: 0.7134 (m-30) REVERT: A 595 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8119 (tmmt) REVERT: A 615 LYS cc_start: 0.8003 (tppt) cc_final: 0.7620 (tptp) REVERT: A 695 ARG cc_start: 0.7756 (mmm-85) cc_final: 0.7555 (mmm-85) REVERT: A 754 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7512 (tm-30) REVERT: A 766 ARG cc_start: 0.7420 (ttm170) cc_final: 0.7080 (mtt180) REVERT: A 811 GLU cc_start: 0.6397 (tm-30) cc_final: 0.6033 (tp30) REVERT: A 888 SER cc_start: 0.8289 (t) cc_final: 0.8038 (p) REVERT: B 130 ASN cc_start: 0.8321 (m-40) cc_final: 0.8087 (m-40) REVERT: B 143 TYR cc_start: 0.8464 (p90) cc_final: 0.7985 (p90) REVERT: B 157 MET cc_start: 0.7159 (OUTLIER) cc_final: 0.6690 (mmm) REVERT: C 13 ASN cc_start: 0.8617 (p0) cc_final: 0.8360 (p0) REVERT: C 79 VAL cc_start: 0.9003 (t) cc_final: 0.8664 (m) REVERT: C 112 VAL cc_start: 0.8899 (p) cc_final: 0.8682 (t) REVERT: C 228 ASP cc_start: 0.7798 (p0) cc_final: 0.7461 (p0) outliers start: 39 outliers final: 15 residues processed: 270 average time/residue: 1.3010 time to fit residues: 376.2319 Evaluate side-chains 267 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 248 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 173 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 0.8980 chunk 115 optimal weight: 0.6980 chunk 67 optimal weight: 0.0770 chunk 48 optimal weight: 0.8980 chunk 88 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 106 optimal weight: 0.9980 chunk 111 optimal weight: 0.5980 chunk 73 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 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 270 ASN A 376 GLN A 826 HIS B 36 GLN ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 HIS ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 GLN C 73 ASN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10283 Z= 0.268 Angle : 0.720 14.048 13920 Z= 0.355 Chirality : 0.045 0.205 1603 Planarity : 0.005 0.049 1761 Dihedral : 4.437 19.038 1338 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.30 % Allowed : 28.67 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.23 (0.25), residues: 1237 helix: 1.55 (0.21), residues: 630 sheet: 0.64 (0.38), residues: 194 loop : -0.14 (0.32), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 6 HIS 0.006 0.001 HIS B 90 PHE 0.043 0.002 PHE A 358 TYR 0.018 0.001 TYR B 167 ARG 0.011 0.001 ARG A 631 *********************** 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 287 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 261 time to evaluate : 1.191 Fit side-chains revert: symmetry clash REVERT: A 202 ASP cc_start: 0.7718 (OUTLIER) cc_final: 0.7476 (t70) REVERT: A 288 ARG cc_start: 0.8146 (ttt180) cc_final: 0.7766 (ttt-90) REVERT: A 345 GLU cc_start: 0.7309 (pp20) cc_final: 0.6800 (pp20) REVERT: A 416 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6688 (mp0) REVERT: A 561 SER cc_start: 0.8641 (m) cc_final: 0.8176 (t) REVERT: A 591 ASP cc_start: 0.7385 (m-30) cc_final: 0.7141 (m-30) REVERT: A 595 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8117 (tmmt) REVERT: A 615 LYS cc_start: 0.8092 (tppt) cc_final: 0.7700 (tptp) REVERT: A 643 MET cc_start: 0.8577 (tpp) cc_final: 0.8317 (mmm) REVERT: A 663 MET cc_start: 0.7925 (tmm) cc_final: 0.7621 (tmm) REVERT: A 695 ARG cc_start: 0.7738 (mmm-85) cc_final: 0.7516 (mmm-85) REVERT: A 754 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7590 (tp30) REVERT: A 811 GLU cc_start: 0.6423 (tm-30) cc_final: 0.6038 (tp30) REVERT: A 888 SER cc_start: 0.8131 (t) cc_final: 0.7918 (p) REVERT: B 143 TYR cc_start: 0.8436 (p90) cc_final: 0.7970 (p90) REVERT: C 13 ASN cc_start: 0.8603 (p0) cc_final: 0.8368 (p0) REVERT: C 79 VAL cc_start: 0.9005 (t) cc_final: 0.8675 (m) REVERT: C 112 VAL cc_start: 0.8892 (p) cc_final: 0.8684 (t) REVERT: C 134 THR cc_start: 0.7942 (p) cc_final: 0.7739 (m) REVERT: C 210 GLU cc_start: 0.8171 (pt0) cc_final: 0.7674 (pt0) REVERT: C 228 ASP cc_start: 0.7750 (p0) cc_final: 0.7405 (p0) REVERT: C 231 GLU cc_start: 0.7493 (pt0) cc_final: 0.7290 (pt0) outliers start: 26 outliers final: 16 residues processed: 273 average time/residue: 1.4045 time to fit residues: 409.8354 Evaluate side-chains 276 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 257 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 532 HIS Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 147 LYS Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 173 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 72 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 114 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 60 optimal weight: 0.3980 chunk 78 optimal weight: 0.8980 chunk 105 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN A 376 GLN ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 ASN C 70 GLN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10283 Z= 0.304 Angle : 0.744 14.414 13920 Z= 0.367 Chirality : 0.045 0.162 1603 Planarity : 0.005 0.044 1761 Dihedral : 4.507 19.154 1338 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.39 % Allowed : 28.32 % Favored : 69.29 % 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: 1.13 (0.25), residues: 1237 helix: 1.48 (0.21), residues: 630 sheet: 0.50 (0.37), residues: 200 loop : -0.16 (0.33), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 6 HIS 0.006 0.001 HIS B 90 PHE 0.041 0.002 PHE A 358 TYR 0.019 0.002 TYR B 167 ARG 0.010 0.001 ARG A 819 ********************** 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 285 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 258 time to evaluate : 1.188 Fit side-chains revert: symmetry clash REVERT: A 202 ASP cc_start: 0.7782 (OUTLIER) cc_final: 0.7524 (t70) REVERT: A 288 ARG cc_start: 0.8145 (ttt180) cc_final: 0.7750 (ttt-90) REVERT: A 345 GLU cc_start: 0.7313 (pp20) cc_final: 0.6806 (pp20) REVERT: A 416 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6704 (mp0) REVERT: A 591 ASP cc_start: 0.7402 (m-30) cc_final: 0.7149 (m-30) REVERT: A 595 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8117 (tmmt) REVERT: A 615 LYS cc_start: 0.8122 (tppt) cc_final: 0.7673 (tptp) REVERT: A 643 MET cc_start: 0.8645 (tpp) cc_final: 0.8368 (mmm) REVERT: A 663 MET cc_start: 0.7953 (tmm) cc_final: 0.7553 (tmm) REVERT: A 766 ARG cc_start: 0.7387 (ttm170) cc_final: 0.7062 (mtt180) REVERT: A 811 GLU cc_start: 0.6435 (tm-30) cc_final: 0.6036 (tp30) REVERT: A 873 GLU cc_start: 0.6995 (pp20) cc_final: 0.6756 (pp20) REVERT: A 888 SER cc_start: 0.8149 (t) cc_final: 0.7924 (p) REVERT: B 4 HIS cc_start: 0.6786 (OUTLIER) cc_final: 0.6501 (m-70) REVERT: B 73 TYR cc_start: 0.8158 (m-10) cc_final: 0.7844 (m-10) REVERT: B 143 TYR cc_start: 0.8425 (p90) cc_final: 0.7970 (p90) REVERT: B 180 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7853 (mtp85) REVERT: C 13 ASN cc_start: 0.8594 (p0) cc_final: 0.8368 (p0) REVERT: C 79 VAL cc_start: 0.9004 (t) cc_final: 0.8693 (m) REVERT: C 112 VAL cc_start: 0.8892 (p) cc_final: 0.8678 (t) REVERT: C 210 GLU cc_start: 0.8178 (pt0) cc_final: 0.7673 (pt0) REVERT: C 228 ASP cc_start: 0.7842 (p0) cc_final: 0.7614 (p0) outliers start: 27 outliers final: 18 residues processed: 268 average time/residue: 1.3451 time to fit residues: 385.2842 Evaluate side-chains 271 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 249 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 532 HIS Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain B residue 4 HIS Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 180 ARG Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 147 LYS Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 200 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 30 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 99 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 12 optimal weight: 0.1980 chunk 18 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN A 369 HIS A 376 GLN B 36 GLN ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 ASN C 70 GLN C 73 ASN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.131654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.120295 restraints weight = 17725.051| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.48 r_work: 0.3569 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10283 Z= 0.297 Angle : 0.751 14.402 13920 Z= 0.371 Chirality : 0.046 0.198 1603 Planarity : 0.005 0.044 1761 Dihedral : 4.496 19.132 1338 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.30 % Allowed : 28.94 % Favored : 68.76 % 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: 1.15 (0.24), residues: 1237 helix: 1.51 (0.21), residues: 627 sheet: 0.48 (0.37), residues: 200 loop : -0.14 (0.33), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 6 HIS 0.006 0.001 HIS B 90 PHE 0.045 0.002 PHE A 358 TYR 0.016 0.002 TYR B 73 ARG 0.011 0.001 ARG A 819 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5564.00 seconds wall clock time: 99 minutes 43.31 seconds (5983.31 seconds total)