Starting phenix.real_space_refine on Sat Jul 20 05:36:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syn_40885/07_2024/8syn_40885.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syn_40885/07_2024/8syn_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syn_40885/07_2024/8syn_40885.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syn_40885/07_2024/8syn_40885.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syn_40885/07_2024/8syn_40885.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syn_40885/07_2024/8syn_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 Residue "A TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 220": "OD1" <-> "OD2" Residue "A ASP 236": "OD1" <-> "OD2" Residue "A ASP 559": "OD1" <-> "OD2" Residue "A ASP 619": "OD1" <-> "OD2" Residue "A PHE 646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 668": "OE1" <-> "OE2" Residue "B PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 283": "OD1" <-> "OD2" Residue "C PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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 - 3.50 Amino acid : False - 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: 4.30 Conformation dependent library (CDL) restraints added in 1.8 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: 1.22 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: 3.86 Time building geometry restraints manager: 4.70 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: 98.42 - 105.53: 185 105.53 - 112.64: 5561 112.64 - 119.76: 3273 119.76 - 126.87: 4782 126.87 - 133.98: 119 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 2.520 nonbonded pdb=" OH TYR A 387 " pdb=" OH TYR A 391 " model vdw 2.211 2.440 nonbonded pdb=" OE2 GLU A 297 " pdb=" NH2 ARG A 318 " model vdw 2.215 2.520 nonbonded pdb=" O PRO A 34 " pdb=" NZ LYS B 34 " model vdw 2.217 2.520 nonbonded pdb=" O PHE A 656 " pdb=" OG SER A 660 " model vdw 2.232 2.440 ... (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 ========== 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: 2.750 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: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 32.020 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 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:11.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.820 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 1.001 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: 1.1315 time to fit residues: 321.9824 Evaluate side-chains 238 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 1.161 ------------------------------------------------------------------------------- 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: 0.9990 chunk 94 optimal weight: 0.0370 chunk 52 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 63 optimal weight: 0.0020 chunk 50 optimal weight: 6.9990 chunk 97 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 59 optimal weight: 0.1980 chunk 72 optimal weight: 40.0000 chunk 113 optimal weight: 0.8980 overall best weight: 0.3266 ------------------------------------------------------------------------------- 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 A 911 GLN C 115 ASN C 117 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6794 moved from start: 0.1166 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= 0.214 Angle : 0.590 7.469 13920 Z= 0.301 Chirality : 0.043 0.145 1603 Planarity : 0.004 0.059 1761 Dihedral : 4.232 19.243 1338 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.68 % Allowed : 10.35 % Favored : 87.96 % 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: 1.62 (0.21), residues: 624 sheet: 0.52 (0.39), residues: 195 loop : -0.00 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 810 HIS 0.009 0.001 HIS B 90 PHE 0.024 0.002 PHE A 796 TYR 0.029 0.002 TYR B 73 ARG 0.002 0.000 ARG B 64 *********************** 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 265 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 246 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 ASP cc_start: 0.7628 (t0) cc_final: 0.7399 (t0) REVERT: A 344 MET cc_start: 0.8524 (mmt) cc_final: 0.8071 (tpp) REVERT: A 366 LYS cc_start: 0.7782 (tptp) cc_final: 0.7441 (tppt) REVERT: A 419 LYS cc_start: 0.7848 (ttpt) cc_final: 0.7561 (ttmt) REVERT: A 488 GLU cc_start: 0.7743 (tp30) cc_final: 0.7454 (mm-30) REVERT: A 501 ASP cc_start: 0.7293 (p0) cc_final: 0.7092 (p0) REVERT: A 514 CYS cc_start: 0.8034 (m) cc_final: 0.7612 (m) REVERT: A 551 LYS cc_start: 0.7432 (mttm) cc_final: 0.7161 (mttm) REVERT: A 584 GLU cc_start: 0.6786 (tm-30) cc_final: 0.6481 (tm-30) REVERT: A 595 LYS cc_start: 0.8490 (tmmt) cc_final: 0.7955 (tmmm) REVERT: A 596 HIS cc_start: 0.8003 (m170) cc_final: 0.7599 (m-70) REVERT: A 630 LYS cc_start: 0.7617 (mttp) cc_final: 0.7216 (mtmm) REVERT: A 652 GLN cc_start: 0.7245 (OUTLIER) cc_final: 0.6914 (tp-100) REVERT: A 659 GLU cc_start: 0.6627 (pp20) cc_final: 0.6229 (tm-30) REVERT: A 661 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7540 (ttm110) REVERT: A 666 ASN cc_start: 0.7243 (t0) cc_final: 0.7032 (t0) REVERT: A 868 MET cc_start: 0.5476 (mtm) cc_final: 0.4969 (mtm) REVERT: B 176 VAL cc_start: 0.8275 (OUTLIER) cc_final: 0.8043 (m) REVERT: C 14 LYS cc_start: 0.8546 (mtmt) cc_final: 0.8257 (mtmt) REVERT: C 43 MET cc_start: 0.8370 (tmm) cc_final: 0.8079 (ttm) REVERT: C 44 GLU cc_start: 0.8017 (tt0) cc_final: 0.7791 (tt0) REVERT: C 175 LYS cc_start: 0.8167 (mppt) cc_final: 0.7900 (mppt) REVERT: C 176 PHE cc_start: 0.7967 (p90) cc_final: 0.7724 (p90) REVERT: C 203 GLU cc_start: 0.7453 (tt0) cc_final: 0.7064 (tt0) REVERT: C 231 GLU cc_start: 0.7455 (pt0) cc_final: 0.7226 (pt0) REVERT: C 269 LYS cc_start: 0.8247 (mtmm) cc_final: 0.7962 (mtmm) REVERT: C 290 PHE cc_start: 0.8370 (m-80) cc_final: 0.8127 (m-80) outliers start: 19 outliers final: 7 residues processed: 254 average time/residue: 1.0269 time to fit residues: 283.1199 Evaluate side-chains 248 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 238 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 ASP 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 B residue 168 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 277 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 77 optimal weight: 40.0000 chunk 31 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 112 optimal weight: 5.9990 chunk 38 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 727 HIS B 170 GLN C 115 ASN C 234 ASN C 289 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 10283 Z= 0.310 Angle : 0.597 8.145 13920 Z= 0.304 Chirality : 0.044 0.155 1603 Planarity : 0.004 0.053 1761 Dihedral : 4.270 18.997 1338 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.48 % Allowed : 13.89 % Favored : 83.63 % 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: 1.41 (0.25), residues: 1237 helix: 1.76 (0.21), residues: 622 sheet: 0.44 (0.39), residues: 195 loop : 0.03 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 810 HIS 0.007 0.001 HIS A 596 PHE 0.038 0.002 PHE A 796 TYR 0.022 0.002 TYR A 821 ARG 0.004 0.000 ARG A 127 *********************** 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 276 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 248 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 ASP cc_start: 0.7582 (t0) cc_final: 0.7274 (t0) REVERT: A 352 GLU cc_start: 0.6456 (tm-30) cc_final: 0.6207 (tm-30) REVERT: A 366 LYS cc_start: 0.7790 (tptp) cc_final: 0.7440 (tppt) REVERT: A 419 LYS cc_start: 0.7888 (ttpt) cc_final: 0.7555 (ttmp) REVERT: A 488 GLU cc_start: 0.7783 (tp30) cc_final: 0.7506 (mm-30) REVERT: A 501 ASP cc_start: 0.7315 (p0) cc_final: 0.7106 (p0) REVERT: A 551 LYS cc_start: 0.7526 (mttm) cc_final: 0.7252 (mttm) REVERT: A 574 ASP cc_start: 0.7463 (t70) cc_final: 0.7258 (t0) REVERT: A 584 GLU cc_start: 0.6761 (tm-30) cc_final: 0.6464 (tm-30) REVERT: A 590 MET cc_start: 0.8132 (mmm) cc_final: 0.7793 (tpt) REVERT: A 595 LYS cc_start: 0.8507 (tmmt) cc_final: 0.7836 (tmmm) REVERT: A 630 LYS cc_start: 0.7651 (mttp) cc_final: 0.7314 (mtmm) REVERT: A 659 GLU cc_start: 0.6689 (pp20) cc_final: 0.6280 (tm-30) REVERT: A 661 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7548 (ttm110) REVERT: A 666 ASN cc_start: 0.7371 (t0) cc_final: 0.7098 (t0) REVERT: A 868 MET cc_start: 0.5519 (mtm) cc_final: 0.5012 (mtm) REVERT: B 122 LYS cc_start: 0.7854 (tmmt) cc_final: 0.7633 (tmmt) REVERT: B 176 VAL cc_start: 0.8356 (OUTLIER) cc_final: 0.8136 (m) REVERT: C 44 GLU cc_start: 0.8051 (tt0) cc_final: 0.7793 (tt0) REVERT: C 175 LYS cc_start: 0.8198 (mppt) cc_final: 0.7943 (mppt) REVERT: C 176 PHE cc_start: 0.8152 (p90) cc_final: 0.7939 (p90) REVERT: C 203 GLU cc_start: 0.7466 (tt0) cc_final: 0.7084 (tt0) REVERT: C 231 GLU cc_start: 0.7481 (pt0) cc_final: 0.7266 (pt0) REVERT: C 269 LYS cc_start: 0.8265 (mtmm) cc_final: 0.7978 (mtmm) REVERT: C 290 PHE cc_start: 0.8397 (m-80) cc_final: 0.8143 (m-80) outliers start: 28 outliers final: 13 residues processed: 257 average time/residue: 1.0604 time to fit residues: 294.5465 Evaluate side-chains 258 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 243 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 661 ARG Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 277 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 59 optimal weight: 0.3980 chunk 12 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 76 optimal weight: 20.0000 chunk 114 optimal weight: 0.7980 chunk 120 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 ASN A 727 HIS B 128 HIS C 115 ASN C 289 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10283 Z= 0.287 Angle : 0.600 13.952 13920 Z= 0.304 Chirality : 0.044 0.172 1603 Planarity : 0.004 0.049 1761 Dihedral : 4.251 18.279 1338 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.01 % Allowed : 16.02 % Favored : 80.97 % 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: 1.46 (0.25), residues: 1237 helix: 1.81 (0.21), residues: 622 sheet: 0.49 (0.39), residues: 195 loop : 0.04 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 490 HIS 0.007 0.001 HIS A 596 PHE 0.043 0.002 PHE A 796 TYR 0.031 0.002 TYR B 73 ARG 0.003 0.000 ARG A 417 *********************** 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 277 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 243 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 ASP cc_start: 0.7637 (t0) cc_final: 0.7307 (t0) REVERT: A 352 GLU cc_start: 0.6545 (tm-30) cc_final: 0.6234 (tm-30) REVERT: A 416 GLU cc_start: 0.7406 (mm-30) cc_final: 0.6861 (mm-30) REVERT: A 419 LYS cc_start: 0.7907 (ttpt) cc_final: 0.7614 (ttmt) REVERT: A 488 GLU cc_start: 0.7867 (tp30) cc_final: 0.7587 (mm-30) REVERT: A 501 ASP cc_start: 0.7319 (p0) cc_final: 0.7086 (p0) REVERT: A 551 LYS cc_start: 0.7554 (mttm) cc_final: 0.7287 (mttm) REVERT: A 567 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7379 (mp0) REVERT: A 584 GLU cc_start: 0.6786 (tm-30) cc_final: 0.6479 (tm-30) REVERT: A 590 MET cc_start: 0.8119 (mmm) cc_final: 0.7731 (tpt) REVERT: A 595 LYS cc_start: 0.8549 (tmmt) cc_final: 0.8050 (tttm) REVERT: A 630 LYS cc_start: 0.7662 (mttp) cc_final: 0.7460 (mtmm) REVERT: A 632 MET cc_start: 0.7650 (OUTLIER) cc_final: 0.7328 (ttm) REVERT: A 637 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8395 (mp) REVERT: A 659 GLU cc_start: 0.6791 (pp20) cc_final: 0.6394 (tm-30) REVERT: A 666 ASN cc_start: 0.7381 (t0) cc_final: 0.7102 (t0) REVERT: A 800 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6769 (mp0) REVERT: A 868 MET cc_start: 0.5523 (mtm) cc_final: 0.5011 (mtm) REVERT: B 176 VAL cc_start: 0.8366 (OUTLIER) cc_final: 0.8142 (m) REVERT: C 14 LYS cc_start: 0.8557 (mtmt) cc_final: 0.8313 (mtmt) REVERT: C 44 GLU cc_start: 0.8052 (tt0) cc_final: 0.7825 (tt0) REVERT: C 95 PHE cc_start: 0.8295 (m-80) cc_final: 0.7985 (m-80) REVERT: C 175 LYS cc_start: 0.8211 (mppt) cc_final: 0.7881 (mppt) REVERT: C 176 PHE cc_start: 0.8214 (p90) cc_final: 0.7814 (p90) REVERT: C 203 GLU cc_start: 0.7470 (tt0) cc_final: 0.7041 (tt0) REVERT: C 231 GLU cc_start: 0.7494 (pt0) cc_final: 0.7224 (pt0) REVERT: C 269 LYS cc_start: 0.8234 (mtmm) cc_final: 0.7943 (mtmm) REVERT: C 290 PHE cc_start: 0.8385 (m-80) cc_final: 0.8134 (m-80) outliers start: 34 outliers final: 15 residues processed: 253 average time/residue: 1.0859 time to fit residues: 298.8159 Evaluate side-chains 258 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 239 time to evaluate : 1.147 ------------------------------------------------------------------------------- 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 371 ASP Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 202 SER 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 68 optimal weight: 0.8980 chunk 1 optimal weight: 20.0000 chunk 89 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 0 optimal weight: 70.0000 chunk 61 optimal weight: 4.9990 chunk 108 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 727 HIS C 115 ASN C 289 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 10283 Z= 0.347 Angle : 0.630 10.425 13920 Z= 0.317 Chirality : 0.045 0.181 1603 Planarity : 0.004 0.048 1761 Dihedral : 4.327 18.494 1338 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.83 % Allowed : 17.17 % Favored : 80.00 % 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: 1.34 (0.25), residues: 1237 helix: 1.69 (0.21), residues: 624 sheet: 0.40 (0.39), residues: 195 loop : 0.04 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 490 HIS 0.007 0.001 HIS A 596 PHE 0.030 0.002 PHE A 796 TYR 0.026 0.002 TYR B 73 ARG 0.004 0.000 ARG A 686 *********************** 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 274 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 242 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7030 (mp0) REVERT: A 202 ASP cc_start: 0.7649 (t0) cc_final: 0.7319 (t0) REVERT: A 352 GLU cc_start: 0.6621 (tm-30) cc_final: 0.6276 (tm-30) REVERT: A 416 GLU cc_start: 0.7413 (mm-30) cc_final: 0.6949 (mp0) REVERT: A 419 LYS cc_start: 0.7918 (ttpt) cc_final: 0.7619 (ttmt) REVERT: A 488 GLU cc_start: 0.7878 (tp30) cc_final: 0.7574 (mm-30) REVERT: A 497 LYS cc_start: 0.8277 (mmtp) cc_final: 0.8038 (mmtp) REVERT: A 551 LYS cc_start: 0.7554 (mttm) cc_final: 0.7299 (mttm) REVERT: A 567 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7368 (mp0) REVERT: A 584 GLU cc_start: 0.6785 (tm-30) cc_final: 0.6506 (tm-30) REVERT: A 590 MET cc_start: 0.8138 (mmm) cc_final: 0.7736 (tpt) REVERT: A 595 LYS cc_start: 0.8535 (tmmt) cc_final: 0.8010 (tttm) REVERT: A 599 GLU cc_start: 0.7781 (pm20) cc_final: 0.7540 (mp0) REVERT: A 630 LYS cc_start: 0.7739 (mttp) cc_final: 0.7524 (mtmm) REVERT: A 637 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8303 (mp) REVERT: A 659 GLU cc_start: 0.6890 (pp20) cc_final: 0.6297 (tm-30) REVERT: A 663 MET cc_start: 0.8011 (ttm) cc_final: 0.7795 (ttm) REVERT: A 666 ASN cc_start: 0.7372 (t0) cc_final: 0.7044 (t0) REVERT: A 686 ARG cc_start: 0.6402 (tmm160) cc_final: 0.6139 (tmm160) REVERT: A 868 MET cc_start: 0.5509 (mtm) cc_final: 0.5012 (mtm) REVERT: B 176 VAL cc_start: 0.8354 (OUTLIER) cc_final: 0.8132 (m) REVERT: C 14 LYS cc_start: 0.8569 (mtmt) cc_final: 0.8362 (mtmt) REVERT: C 43 MET cc_start: 0.8377 (tmm) cc_final: 0.8151 (ttm) REVERT: C 44 GLU cc_start: 0.8070 (tt0) cc_final: 0.7859 (tt0) REVERT: C 95 PHE cc_start: 0.8284 (m-80) cc_final: 0.7964 (m-80) REVERT: C 175 LYS cc_start: 0.8218 (mppt) cc_final: 0.7857 (mppt) REVERT: C 176 PHE cc_start: 0.8265 (p90) cc_final: 0.7870 (p90) REVERT: C 203 GLU cc_start: 0.7476 (tt0) cc_final: 0.6912 (tt0) REVERT: C 231 GLU cc_start: 0.7510 (pt0) cc_final: 0.7237 (pt0) REVERT: C 269 LYS cc_start: 0.8231 (mtmm) cc_final: 0.7956 (mtmm) REVERT: C 290 PHE cc_start: 0.8384 (m-80) cc_final: 0.8158 (m-80) outliers start: 32 outliers final: 21 residues processed: 250 average time/residue: 1.0407 time to fit residues: 282.0873 Evaluate side-chains 257 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 233 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain B residue 81 VAL 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 B residue 176 VAL Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 202 SER 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 108 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 70 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 120 optimal weight: 0.6980 chunk 100 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 652 GLN A 727 HIS ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN C 289 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10283 Z= 0.271 Angle : 0.606 9.863 13920 Z= 0.304 Chirality : 0.044 0.154 1603 Planarity : 0.004 0.047 1761 Dihedral : 4.284 21.615 1338 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.10 % Allowed : 18.14 % Favored : 78.76 % 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: 1.41 (0.25), residues: 1237 helix: 1.75 (0.21), residues: 625 sheet: 0.39 (0.39), residues: 195 loop : 0.08 (0.32), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 490 HIS 0.006 0.001 HIS A 596 PHE 0.019 0.002 PHE A 745 TYR 0.025 0.002 TYR B 143 ARG 0.003 0.000 ARG A 127 *********************** 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 281 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 246 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6928 (mp0) REVERT: A 202 ASP cc_start: 0.7605 (t0) cc_final: 0.7302 (t0) REVERT: A 318 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.6891 (ttm170) REVERT: A 352 GLU cc_start: 0.6594 (tm-30) cc_final: 0.6254 (tm-30) REVERT: A 416 GLU cc_start: 0.7372 (mm-30) cc_final: 0.7107 (mm-30) REVERT: A 419 LYS cc_start: 0.7925 (ttpt) cc_final: 0.7620 (ttmt) REVERT: A 488 GLU cc_start: 0.7876 (tp30) cc_final: 0.7561 (mm-30) REVERT: A 497 LYS cc_start: 0.8280 (mmtp) cc_final: 0.8036 (mmtp) REVERT: A 551 LYS cc_start: 0.7566 (mttm) cc_final: 0.7298 (mttm) REVERT: A 584 GLU cc_start: 0.6774 (tm-30) cc_final: 0.6467 (tm-30) REVERT: A 590 MET cc_start: 0.8137 (mmm) cc_final: 0.7760 (tpt) REVERT: A 595 LYS cc_start: 0.8492 (tmmt) cc_final: 0.7977 (tttm) REVERT: A 599 GLU cc_start: 0.7755 (pm20) cc_final: 0.7478 (mp0) REVERT: A 637 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8346 (mp) REVERT: A 643 MET cc_start: 0.8499 (mmm) cc_final: 0.8188 (mmt) REVERT: A 659 GLU cc_start: 0.7058 (pp20) cc_final: 0.6495 (tm-30) REVERT: A 663 MET cc_start: 0.8014 (ttm) cc_final: 0.7801 (ttm) REVERT: A 666 ASN cc_start: 0.7357 (t0) cc_final: 0.7031 (t0) REVERT: A 668 GLU cc_start: 0.7396 (tt0) cc_final: 0.7156 (tt0) REVERT: A 686 ARG cc_start: 0.6420 (tmm160) cc_final: 0.6168 (tmm160) REVERT: A 868 MET cc_start: 0.5506 (mtm) cc_final: 0.5012 (mtm) REVERT: B 176 VAL cc_start: 0.8349 (OUTLIER) cc_final: 0.8123 (m) REVERT: C 14 LYS cc_start: 0.8547 (mtmt) cc_final: 0.8281 (mtmt) REVERT: C 44 GLU cc_start: 0.8063 (tt0) cc_final: 0.7847 (tt0) REVERT: C 95 PHE cc_start: 0.8226 (m-80) cc_final: 0.7901 (m-80) REVERT: C 176 PHE cc_start: 0.8248 (p90) cc_final: 0.7921 (p90) REVERT: C 231 GLU cc_start: 0.7489 (pt0) cc_final: 0.7214 (pt0) REVERT: C 269 LYS cc_start: 0.8213 (mtmm) cc_final: 0.7947 (mtmm) REVERT: C 290 PHE cc_start: 0.8358 (m-80) cc_final: 0.8130 (m-80) outliers start: 35 outliers final: 17 residues processed: 258 average time/residue: 1.0488 time to fit residues: 293.2150 Evaluate side-chains 267 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 246 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 476 ASP 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 637 ILE Chi-restraints excluded: chain A residue 652 GLN Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain B residue 81 VAL 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 B residue 176 VAL Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 202 SER 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 13 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 chunk 75 optimal weight: 50.0000 chunk 73 optimal weight: 9.9990 chunk 55 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 48 optimal weight: 0.0870 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 727 HIS ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN C 289 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 10283 Z= 0.303 Angle : 0.641 15.144 13920 Z= 0.318 Chirality : 0.045 0.213 1603 Planarity : 0.004 0.047 1761 Dihedral : 4.314 21.012 1338 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.45 % Allowed : 18.58 % Favored : 77.96 % 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 (0.25), residues: 1237 helix: 1.63 (0.21), residues: 626 sheet: 0.36 (0.39), residues: 195 loop : 0.02 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 490 HIS 0.006 0.001 HIS A 596 PHE 0.021 0.002 PHE C 113 TYR 0.038 0.002 TYR B 73 ARG 0.004 0.000 ARG A 127 *********************** 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 284 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 245 time to evaluate : 1.177 Fit side-chains revert: symmetry clash REVERT: A 115 GLU cc_start: 0.6938 (tp30) cc_final: 0.6737 (tp30) REVERT: A 123 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6935 (mp0) REVERT: A 202 ASP cc_start: 0.7610 (t0) cc_final: 0.7334 (t0) REVERT: A 248 ARG cc_start: 0.7031 (tpt90) cc_final: 0.6418 (tpt90) REVERT: A 252 MET cc_start: 0.8197 (mtt) cc_final: 0.7121 (mtt) REVERT: A 352 GLU cc_start: 0.6627 (tm-30) cc_final: 0.6273 (tm-30) REVERT: A 416 GLU cc_start: 0.7367 (mm-30) cc_final: 0.7092 (mm-30) REVERT: A 419 LYS cc_start: 0.7929 (ttpt) cc_final: 0.7635 (ttmt) REVERT: A 488 GLU cc_start: 0.7899 (tp30) cc_final: 0.7553 (mm-30) REVERT: A 497 LYS cc_start: 0.8277 (mmtp) cc_final: 0.8031 (mmtp) REVERT: A 551 LYS cc_start: 0.7593 (mttm) cc_final: 0.7324 (mttm) REVERT: A 567 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7661 (mp0) REVERT: A 584 GLU cc_start: 0.6783 (tm-30) cc_final: 0.6482 (tm-30) REVERT: A 590 MET cc_start: 0.8145 (mmm) cc_final: 0.7763 (tpt) REVERT: A 595 LYS cc_start: 0.8498 (tmmt) cc_final: 0.7950 (tttm) REVERT: A 599 GLU cc_start: 0.7756 (pm20) cc_final: 0.7496 (mp0) REVERT: A 637 ILE cc_start: 0.8639 (OUTLIER) cc_final: 0.8352 (mp) REVERT: A 643 MET cc_start: 0.8529 (mmm) cc_final: 0.8192 (mmt) REVERT: A 659 GLU cc_start: 0.7169 (pp20) cc_final: 0.6701 (tm-30) REVERT: A 666 ASN cc_start: 0.7395 (t0) cc_final: 0.7036 (t0) REVERT: A 668 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.7199 (tt0) REVERT: A 868 MET cc_start: 0.5519 (mtm) cc_final: 0.5026 (mtm) REVERT: B 176 VAL cc_start: 0.8314 (OUTLIER) cc_final: 0.8089 (m) REVERT: C 14 LYS cc_start: 0.8543 (mtmt) cc_final: 0.8271 (mtmt) REVERT: C 42 THR cc_start: 0.8588 (m) cc_final: 0.8219 (p) REVERT: C 44 GLU cc_start: 0.8077 (tt0) cc_final: 0.7855 (tt0) REVERT: C 95 PHE cc_start: 0.8174 (m-80) cc_final: 0.7722 (m-80) REVERT: C 176 PHE cc_start: 0.8264 (p90) cc_final: 0.7886 (p90) REVERT: C 228 ASP cc_start: 0.7564 (OUTLIER) cc_final: 0.7277 (p0) REVERT: C 231 GLU cc_start: 0.7487 (pt0) cc_final: 0.7219 (pt0) REVERT: C 269 LYS cc_start: 0.8214 (mtmm) cc_final: 0.7951 (mtmm) REVERT: C 290 PHE cc_start: 0.8347 (m-80) cc_final: 0.8125 (m-80) outliers start: 39 outliers final: 22 residues processed: 260 average time/residue: 1.0594 time to fit residues: 298.4210 Evaluate side-chains 269 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 242 time to evaluate : 1.076 ------------------------------------------------------------------------------- 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 371 ASP Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 532 HIS Chi-restraints excluded: chain A residue 534 THR 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 644 VAL Chi-restraints excluded: chain A residue 668 GLU 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 94 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 217 GLU Chi-restraints excluded: chain C residue 228 ASP 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 71 optimal weight: 0.0060 chunk 36 optimal weight: 0.0980 chunk 23 optimal weight: 0.8980 chunk 76 optimal weight: 30.0000 chunk 82 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 11 optimal weight: 0.0870 chunk 94 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 105 optimal weight: 0.5980 overall best weight: 0.3174 ------------------------------------------------------------------------------- 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 516 HIS A 727 HIS ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN C 233 GLN C 289 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 10283 Z= 0.213 Angle : 0.632 14.112 13920 Z= 0.311 Chirality : 0.044 0.198 1603 Planarity : 0.004 0.045 1761 Dihedral : 4.202 20.158 1338 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.39 % Allowed : 20.44 % Favored : 77.17 % 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: 1.45 (0.25), residues: 1237 helix: 1.79 (0.21), residues: 623 sheet: 0.43 (0.39), residues: 190 loop : 0.07 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 490 HIS 0.005 0.001 HIS A 596 PHE 0.019 0.001 PHE B 126 TYR 0.032 0.002 TYR B 73 ARG 0.007 0.000 ARG A 686 *********************** 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 fitting. rotamer outliers: 27 poor density : 248 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 318 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.6774 (ttm170) REVERT: A 352 GLU cc_start: 0.6537 (tm-30) cc_final: 0.6204 (tm-30) REVERT: A 416 GLU cc_start: 0.7362 (mm-30) cc_final: 0.7064 (mm-30) REVERT: A 419 LYS cc_start: 0.7943 (ttpt) cc_final: 0.7644 (ttmt) REVERT: A 453 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7241 (mp0) REVERT: A 488 GLU cc_start: 0.7856 (tp30) cc_final: 0.7505 (mm-30) REVERT: A 551 LYS cc_start: 0.7540 (mttm) cc_final: 0.7189 (mttm) REVERT: A 567 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7594 (mp0) REVERT: A 574 ASP cc_start: 0.7471 (OUTLIER) cc_final: 0.7201 (t0) REVERT: A 584 GLU cc_start: 0.6693 (tm-30) cc_final: 0.6414 (tm-30) REVERT: A 595 LYS cc_start: 0.8481 (tmmt) cc_final: 0.7926 (tttm) REVERT: A 599 GLU cc_start: 0.7748 (pm20) cc_final: 0.7480 (mp0) REVERT: A 637 ILE cc_start: 0.8609 (OUTLIER) cc_final: 0.8378 (mp) REVERT: A 643 MET cc_start: 0.8473 (mmm) cc_final: 0.8152 (mmt) REVERT: A 659 GLU cc_start: 0.7143 (pp20) cc_final: 0.6815 (tm-30) REVERT: A 666 ASN cc_start: 0.7247 (t0) cc_final: 0.6900 (t0) REVERT: A 668 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.7164 (tt0) REVERT: A 771 PHE cc_start: 0.8315 (m-80) cc_final: 0.8013 (m-80) REVERT: A 868 MET cc_start: 0.5508 (mtm) cc_final: 0.5012 (mtm) REVERT: B 176 VAL cc_start: 0.8260 (OUTLIER) cc_final: 0.8036 (m) REVERT: C 14 LYS cc_start: 0.8538 (mtmt) cc_final: 0.8337 (mtmt) REVERT: C 42 THR cc_start: 0.8555 (m) cc_final: 0.8278 (p) REVERT: C 44 GLU cc_start: 0.8056 (tt0) cc_final: 0.7824 (tt0) REVERT: C 95 PHE cc_start: 0.8091 (m-80) cc_final: 0.7655 (m-80) REVERT: C 176 PHE cc_start: 0.8216 (p90) cc_final: 0.7902 (p90) REVERT: C 228 ASP cc_start: 0.7579 (OUTLIER) cc_final: 0.7212 (p0) REVERT: C 231 GLU cc_start: 0.7440 (pt0) cc_final: 0.7182 (pt0) REVERT: C 269 LYS cc_start: 0.8167 (mtmm) cc_final: 0.7906 (mtmm) REVERT: C 290 PHE cc_start: 0.8303 (m-80) cc_final: 0.8066 (m-80) outliers start: 27 outliers final: 16 residues processed: 258 average time/residue: 1.1146 time to fit residues: 309.9909 Evaluate side-chains 255 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 232 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 476 ASP 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 637 ILE Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain B residue 81 VAL 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 B residue 176 VAL Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 228 ASP 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 112 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 101 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 73 optimal weight: 8.9990 chunk 118 optimal weight: 0.3980 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 516 HIS A 727 HIS ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN C 233 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 10283 Z= 0.303 Angle : 0.673 12.848 13920 Z= 0.329 Chirality : 0.045 0.165 1603 Planarity : 0.004 0.047 1761 Dihedral : 4.285 20.307 1338 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.39 % Allowed : 21.86 % Favored : 75.75 % 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: 1.65 (0.21), residues: 624 sheet: 0.42 (0.38), residues: 195 loop : 0.04 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 199 HIS 0.006 0.001 HIS A 596 PHE 0.019 0.002 PHE B 126 TYR 0.029 0.002 TYR B 143 ARG 0.009 0.000 ARG A 686 *********************** 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 259 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 232 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.6930 (mp0) REVERT: A 318 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.6786 (ttm170) REVERT: A 352 GLU cc_start: 0.6616 (tm-30) cc_final: 0.6268 (tm-30) REVERT: A 416 GLU cc_start: 0.7373 (mm-30) cc_final: 0.7071 (mm-30) REVERT: A 419 LYS cc_start: 0.7926 (ttpt) cc_final: 0.7614 (ttmt) REVERT: A 453 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7256 (mp0) REVERT: A 488 GLU cc_start: 0.7889 (tp30) cc_final: 0.7522 (mm-30) REVERT: A 567 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7630 (mp0) REVERT: A 574 ASP cc_start: 0.7501 (OUTLIER) cc_final: 0.7244 (t0) REVERT: A 584 GLU cc_start: 0.6776 (tm-30) cc_final: 0.6487 (tm-30) REVERT: A 595 LYS cc_start: 0.8491 (tmmt) cc_final: 0.7946 (tttm) REVERT: A 599 GLU cc_start: 0.7752 (pm20) cc_final: 0.7499 (mp0) REVERT: A 637 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.8346 (mp) REVERT: A 643 MET cc_start: 0.8459 (mmm) cc_final: 0.8122 (mmt) REVERT: A 659 GLU cc_start: 0.7197 (pp20) cc_final: 0.6788 (tm-30) REVERT: A 666 ASN cc_start: 0.7244 (t0) cc_final: 0.6869 (t0) REVERT: A 668 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.7147 (tt0) REVERT: A 771 PHE cc_start: 0.8310 (m-80) cc_final: 0.7988 (m-80) REVERT: A 868 MET cc_start: 0.5540 (mtm) cc_final: 0.5042 (mtm) REVERT: B 176 VAL cc_start: 0.8212 (OUTLIER) cc_final: 0.8008 (m) REVERT: C 14 LYS cc_start: 0.8482 (mtmt) cc_final: 0.8262 (mtmt) REVERT: C 42 THR cc_start: 0.8474 (m) cc_final: 0.8112 (p) REVERT: C 44 GLU cc_start: 0.8072 (tt0) cc_final: 0.7812 (tt0) REVERT: C 72 ILE cc_start: 0.8690 (tt) cc_final: 0.8408 (pt) REVERT: C 95 PHE cc_start: 0.8149 (m-80) cc_final: 0.7645 (m-80) REVERT: C 113 PHE cc_start: 0.8366 (m-10) cc_final: 0.8099 (m-10) REVERT: C 176 PHE cc_start: 0.8246 (p90) cc_final: 0.7846 (p90) REVERT: C 228 ASP cc_start: 0.7542 (OUTLIER) cc_final: 0.7236 (p0) REVERT: C 231 GLU cc_start: 0.7441 (pt0) cc_final: 0.7190 (pt0) REVERT: C 269 LYS cc_start: 0.8190 (mtmm) cc_final: 0.7926 (mtmm) REVERT: C 290 PHE cc_start: 0.8315 (m-80) cc_final: 0.8106 (m-80) outliers start: 27 outliers final: 16 residues processed: 242 average time/residue: 1.1045 time to fit residues: 289.6523 Evaluate side-chains 257 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 233 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 453 GLU 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 637 ILE Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain B residue 81 VAL 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 B residue 176 VAL Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 228 ASP 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 72 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 82 optimal weight: 0.0770 chunk 124 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 99 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 60 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 chunk 105 optimal weight: 0.1980 overall best weight: 0.4738 ------------------------------------------------------------------------------- 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 ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN C 233 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 moved from start: 0.2291 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= 0.258 Angle : 0.670 13.410 13920 Z= 0.326 Chirality : 0.044 0.177 1603 Planarity : 0.004 0.046 1761 Dihedral : 4.256 18.362 1338 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.57 % Allowed : 21.95 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.69 (0.21), residues: 624 sheet: 0.39 (0.39), residues: 190 loop : -0.02 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 810 HIS 0.005 0.001 HIS A 596 PHE 0.024 0.002 PHE A 745 TYR 0.033 0.002 TYR B 73 ARG 0.008 0.000 ARG A 686 ********************** 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 271 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 242 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.6964 (mp0) REVERT: A 201 SER cc_start: 0.7852 (t) cc_final: 0.7580 (t) REVERT: A 318 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.6776 (ttm170) REVERT: A 352 GLU cc_start: 0.6586 (tm-30) cc_final: 0.6243 (tm-30) REVERT: A 416 GLU cc_start: 0.7364 (mm-30) cc_final: 0.7062 (mm-30) REVERT: A 419 LYS cc_start: 0.7916 (ttpt) cc_final: 0.7608 (ttmt) REVERT: A 453 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7272 (mp0) REVERT: A 488 GLU cc_start: 0.7901 (tp30) cc_final: 0.7508 (mm-30) REVERT: A 567 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7605 (mp0) REVERT: A 574 ASP cc_start: 0.7557 (OUTLIER) cc_final: 0.7305 (t0) REVERT: A 584 GLU cc_start: 0.6772 (tm-30) cc_final: 0.6472 (tm-30) REVERT: A 599 GLU cc_start: 0.7735 (pm20) cc_final: 0.7493 (mp0) REVERT: A 632 MET cc_start: 0.7651 (OUTLIER) cc_final: 0.7336 (ttm) REVERT: A 637 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8364 (mp) REVERT: A 643 MET cc_start: 0.8441 (mmm) cc_final: 0.8109 (mmt) REVERT: A 659 GLU cc_start: 0.7152 (pp20) cc_final: 0.6705 (tm-30) REVERT: A 663 MET cc_start: 0.7944 (ttm) cc_final: 0.7686 (ttm) REVERT: A 666 ASN cc_start: 0.7216 (t0) cc_final: 0.6851 (t0) REVERT: A 668 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.7122 (tt0) REVERT: A 771 PHE cc_start: 0.8297 (m-80) cc_final: 0.7990 (m-80) REVERT: A 868 MET cc_start: 0.5525 (mtm) cc_final: 0.5029 (mtm) REVERT: B 131 LYS cc_start: 0.6950 (mmmm) cc_final: 0.6607 (mmmm) REVERT: B 176 VAL cc_start: 0.8233 (OUTLIER) cc_final: 0.8027 (m) REVERT: C 14 LYS cc_start: 0.8475 (mtmt) cc_final: 0.8266 (mtmt) REVERT: C 42 THR cc_start: 0.8503 (m) cc_final: 0.8217 (p) REVERT: C 44 GLU cc_start: 0.8074 (tt0) cc_final: 0.7838 (tt0) REVERT: C 72 ILE cc_start: 0.8671 (tt) cc_final: 0.8434 (pt) REVERT: C 95 PHE cc_start: 0.8082 (m-80) cc_final: 0.7553 (m-80) REVERT: C 112 VAL cc_start: 0.8629 (p) cc_final: 0.8381 (m) REVERT: C 113 PHE cc_start: 0.8303 (m-10) cc_final: 0.8093 (m-10) REVERT: C 176 PHE cc_start: 0.8227 (p90) cc_final: 0.7882 (p90) REVERT: C 228 ASP cc_start: 0.7548 (OUTLIER) cc_final: 0.7257 (p0) REVERT: C 231 GLU cc_start: 0.7416 (pt0) cc_final: 0.7172 (pt0) REVERT: C 269 LYS cc_start: 0.8172 (mtmm) cc_final: 0.7907 (mtmm) REVERT: C 290 PHE cc_start: 0.8289 (m-80) cc_final: 0.8058 (m-80) outliers start: 29 outliers final: 17 residues processed: 252 average time/residue: 1.1229 time to fit residues: 306.6223 Evaluate side-chains 262 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 236 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 453 GLU 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 668 GLU Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 725 TYR Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 217 GLU Chi-restraints excluded: chain C residue 228 ASP 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 30 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 101 optimal weight: 0.9980 chunk 12 optimal weight: 0.2980 chunk 18 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 chunk 5 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 516 HIS A 652 GLN A 727 HIS A 778 ASN ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN C 233 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.175183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.147290 restraints weight = 15671.167| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 2.46 r_work: 0.3721 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 10283 Z= 0.279 Angle : 0.682 13.038 13920 Z= 0.332 Chirality : 0.046 0.301 1603 Planarity : 0.004 0.049 1761 Dihedral : 4.291 17.171 1338 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.48 % Allowed : 22.12 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.25), residues: 1237 helix: 1.62 (0.21), residues: 625 sheet: 0.36 (0.38), residues: 195 loop : -0.03 (0.32), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 490 HIS 0.005 0.001 HIS A 596 PHE 0.028 0.002 PHE A 745 TYR 0.030 0.002 TYR B 73 ARG 0.007 0.000 ARG A 686 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4751.26 seconds wall clock time: 83 minutes 18.22 seconds (4998.22 seconds total)