Starting phenix.real_space_refine on Mon Mar 11 02:31:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3h_29699/03_2024/8g3h_29699_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3h_29699/03_2024/8g3h_29699.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3h_29699/03_2024/8g3h_29699.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3h_29699/03_2024/8g3h_29699.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3h_29699/03_2024/8g3h_29699_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3h_29699/03_2024/8g3h_29699_neut_updated.pdb" } resolution = 3.6 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= -0.000 sd= 0.019 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: 7 Type Number sf(0) Gaussians Co 1 6.85 5 Zn 1 6.06 5 P 1 5.49 5 S 26 5.16 5 C 4159 2.51 5 N 1125 2.21 5 O 1228 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 38": "NH1" <-> "NH2" Residue "A ARG 43": "NH1" <-> "NH2" Residue "A ARG 48": "NH1" <-> "NH2" Residue "A ARG 63": "NH1" <-> "NH2" Residue "A ARG 84": "NH1" <-> "NH2" Residue "A ARG 86": "NH1" <-> "NH2" Residue "A ARG 91": "NH1" <-> "NH2" Residue "A ARG 114": "NH1" <-> "NH2" Residue "A GLU 128": "OE1" <-> "OE2" Residue "A ARG 132": "NH1" <-> "NH2" Residue "A ARG 135": "NH1" <-> "NH2" Residue "A ARG 178": "NH1" <-> "NH2" Residue "A ARG 182": "NH1" <-> "NH2" Residue "A ARG 200": "NH1" <-> "NH2" Residue "A ARG 207": "NH1" <-> "NH2" Residue "A ARG 268": "NH1" <-> "NH2" Residue "A ARG 276": "NH1" <-> "NH2" Residue "A ARG 288": "NH1" <-> "NH2" Residue "A ARG 293": "NH1" <-> "NH2" Residue "A ARG 305": "NH1" <-> "NH2" Residue "A ARG 331": "NH1" <-> "NH2" Residue "A ARG 340": "NH1" <-> "NH2" Residue "A TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 363": "NH1" <-> "NH2" Residue "A GLU 365": "OE1" <-> "OE2" Residue "A ARG 374": "NH1" <-> "NH2" Residue "A ARG 382": "NH1" <-> "NH2" Residue "A ARG 384": "NH1" <-> "NH2" Residue "A GLU 405": "OE1" <-> "OE2" Residue "A ARG 419": "NH1" <-> "NH2" Residue "A ARG 427": "NH1" <-> "NH2" Residue "A ARG 456": "NH1" <-> "NH2" Residue "A ARG 460": "NH1" <-> "NH2" Residue "A ARG 477": "NH1" <-> "NH2" Residue "A GLU 496": "OE1" <-> "OE2" Residue "A ARG 503": "NH1" <-> "NH2" Residue "A ARG 512": "NH1" <-> "NH2" Residue "A ARG 516": "NH1" <-> "NH2" Residue "A ARG 524": "NH1" <-> "NH2" Residue "A ARG 545": "NH1" <-> "NH2" Residue "A ARG 549": "NH1" <-> "NH2" Residue "A ARG 559": "NH1" <-> "NH2" Residue "A ARG 561": "NH1" <-> "NH2" Residue "A PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 583": "NH1" <-> "NH2" Residue "A ARG 584": "NH1" <-> "NH2" Residue "A ARG 595": "NH1" <-> "NH2" Residue "A ARG 631": "NH1" <-> "NH2" Residue "A ARG 642": "NH1" <-> "NH2" Residue "A GLU 665": "OE1" <-> "OE2" Residue "A ARG 666": "NH1" <-> "NH2" Residue "A ARG 668": "NH1" <-> "NH2" Residue "A ARG 669": "NH1" <-> "NH2" Residue "A ARG 670": "NH1" <-> "NH2" Residue "A ARG 676": "NH1" <-> "NH2" Residue "A ARG 691": "NH1" <-> "NH2" Residue "A ARG 822": "NH1" <-> "NH2" Residue "A ARG 824": "NH1" <-> "NH2" Residue "A ARG 839": "NH1" <-> "NH2" Residue "A TYR 841": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 843": "OE1" <-> "OE2" Residue "A ARG 846": "NH1" <-> "NH2" Residue "A ARG 872": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6541 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 6541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 843, 6541 Unusual residues: {' ZN': 1, 'B12': 1} Classifications: {'peptide': 841, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 39, 'TRANS': 801, None: 2} Not linked: pdbres="THR A 877 " pdbres=" ZN A1201 " Not linked: pdbres=" ZN A1201 " pdbres="B12 A1202 " Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 46 Unsupported chir.volume_sign: {'cros': 1} Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 33 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1673 SG CYS A 256 34.318 42.889 80.873 1.00 12.37 S ATOM 2190 SG CYS A 323 34.049 43.743 84.392 1.00 19.07 S Time building chain proxies: 4.09, per 1000 atoms: 0.63 Number of scatterers: 6541 At special positions: 0 Unit cell: (64.146, 90.8735, 112.256, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Co 1 26.99 S 26 16.00 P 1 15.00 O 1228 8.00 N 1125 7.00 C 4159 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.65 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1201 " pdb="ZN ZN A1201 " - pdb=" SG CYS A 256 " pdb="ZN ZN A1201 " - pdb=" SG CYS A 323 " 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1538 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 37 helices and 8 sheets defined 47.7% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'A' and resid 40 through 47 Processing helix chain 'A' and resid 57 through 62 removed outlier: 3.871A pdb=" N LYS A 62 " --> pdb=" O THR A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 70 Processing helix chain 'A' and resid 82 through 85 No H-bonds generated for 'chain 'A' and resid 82 through 85' Processing helix chain 'A' and resid 87 through 99 removed outlier: 3.958A pdb=" N TYR A 97 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 98 " --> pdb=" O HIS A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 120 removed outlier: 4.392A pdb=" N GLU A 119 " --> pdb=" O HIS A 115 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N TYR A 120 " --> pdb=" O VAL A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 141 Processing helix chain 'A' and resid 166 through 182 removed outlier: 3.630A pdb=" N ALA A 172 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ARG A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLY A 179 " --> pdb=" O GLU A 175 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 213 removed outlier: 3.716A pdb=" N LEU A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 246 removed outlier: 3.682A pdb=" N LEU A 241 " --> pdb=" O GLU A 237 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N SER A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 271 removed outlier: 6.119A pdb=" N ALA A 265 " --> pdb=" O ASP A 261 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N LYS A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 313 removed outlier: 4.352A pdb=" N THR A 312 " --> pdb=" O LEU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 337 removed outlier: 3.509A pdb=" N ALA A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 386 removed outlier: 4.076A pdb=" N LEU A 386 " --> pdb=" O ARG A 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 382 through 386' Processing helix chain 'A' and resid 392 through 405 removed outlier: 4.040A pdb=" N ALA A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 398 " --> pdb=" O GLY A 394 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLN A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL A 403 " --> pdb=" O ALA A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 435 removed outlier: 3.711A pdb=" N LYS A 426 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS A 431 " --> pdb=" O ARG A 427 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N THR A 434 " --> pdb=" O SER A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 454 removed outlier: 3.690A pdb=" N GLU A 451 " --> pdb=" O PRO A 447 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU A 454 " --> pdb=" O MET A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 484 removed outlier: 3.883A pdb=" N LYS A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 521 removed outlier: 3.870A pdb=" N ALA A 510 " --> pdb=" O LYS A 506 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N GLU A 515 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ARG A 516 " --> pdb=" O ARG A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 527 No H-bonds generated for 'chain 'A' and resid 525 through 527' Processing helix chain 'A' and resid 547 through 559 Processing helix chain 'A' and resid 571 through 573 No H-bonds generated for 'chain 'A' and resid 571 through 573' Processing helix chain 'A' and resid 580 through 597 removed outlier: 4.478A pdb=" N LYS A 596 " --> pdb=" O ASP A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 608 No H-bonds generated for 'chain 'A' and resid 606 through 608' Processing helix chain 'A' and resid 617 through 627 Processing helix chain 'A' and resid 636 through 646 Processing helix chain 'A' and resid 663 through 673 Processing helix chain 'A' and resid 679 through 689 Processing helix chain 'A' and resid 692 through 697 Processing helix chain 'A' and resid 699 through 713 removed outlier: 6.001A pdb=" N MET A 704 " --> pdb=" O LEU A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 738 removed outlier: 3.600A pdb=" N ALA A 733 " --> pdb=" O LYS A 729 " (cutoff:3.500A) Proline residue: A 737 - end of helix Processing helix chain 'A' and resid 761 through 773 removed outlier: 3.786A pdb=" N ILE A 769 " --> pdb=" O LEU A 765 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N LEU A 770 " --> pdb=" O VAL A 766 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASN A 773 " --> pdb=" O ILE A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 796 Processing helix chain 'A' and resid 808 through 823 removed outlier: 4.137A pdb=" N GLN A 812 " --> pdb=" O VAL A 808 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR A 820 " --> pdb=" O GLU A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 841 No H-bonds generated for 'chain 'A' and resid 839 through 841' Processing helix chain 'A' and resid 843 through 847 Processing helix chain 'A' and resid 858 through 869 Processing sheet with id= A, first strand: chain 'A' and resid 50 through 52 Processing sheet with id= B, first strand: chain 'A' and resid 104 through 106 removed outlier: 6.135A pdb=" N PHE A 147 " --> pdb=" O ILE A 105 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LEU A 187 " --> pdb=" O GLY A 150 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 251 through 253 removed outlier: 5.689A pdb=" N PHE A 277 " --> pdb=" O VAL A 252 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 288 through 290 Processing sheet with id= E, first strand: chain 'A' and resid 352 through 354 Processing sheet with id= F, first strand: chain 'A' and resid 369 through 372 removed outlier: 3.774A pdb=" N LEU A 569 " --> pdb=" O ALA A 601 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 409 through 412 removed outlier: 7.977A pdb=" N LEU A 412 " --> pdb=" O PRO A 439 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N MET A 441 " --> pdb=" O LEU A 412 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'A' and resid 748 through 751 removed outlier: 5.950A pdb=" N THR A 776 " --> pdb=" O LEU A 749 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N LEU A 751 " --> pdb=" O THR A 776 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N TYR A 778 " --> pdb=" O LEU A 751 " (cutoff:3.500A) No H-bonds generated for sheet with id= H 230 hydrogen bonds defined for protein. 675 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.75 Time building geometry restraints manager: 2.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.33: 1750 1.33 - 1.50: 2012 1.50 - 1.67: 2846 1.67 - 1.84: 47 1.84 - 2.01: 4 Bond restraints: 6659 Sorted by residual: bond pdb=" C3R B12 A1202 " pdb=" O2 B12 A1202 " ideal model delta sigma weight residual 1.426 1.651 -0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C15 B12 A1202 " pdb=" C53 B12 A1202 " ideal model delta sigma weight residual 1.500 1.685 -0.185 2.00e-02 2.50e+03 8.59e+01 bond pdb=" C4 B12 A1202 " pdb=" N21 B12 A1202 " ideal model delta sigma weight residual 1.416 1.235 0.181 2.00e-02 2.50e+03 8.21e+01 bond pdb=" C49 B12 A1202 " pdb=" C50 B12 A1202 " ideal model delta sigma weight residual 1.510 1.337 0.173 2.00e-02 2.50e+03 7.45e+01 bond pdb=" C5R B12 A1202 " pdb=" O8R B12 A1202 " ideal model delta sigma weight residual 1.432 1.267 0.165 2.00e-02 2.50e+03 6.84e+01 ... (remaining 6654 not shown) Histogram of bond angle deviations from ideal: 83.37 - 102.24: 67 102.24 - 121.12: 7122 121.12 - 140.00: 1858 140.00 - 158.88: 0 158.88 - 177.76: 2 Bond angle restraints: 9049 Sorted by residual: angle pdb=" N ALA A 855 " pdb=" CA ALA A 855 " pdb=" C ALA A 855 " ideal model delta sigma weight residual 110.24 83.37 26.87 1.30e+00 5.92e-01 4.27e+02 angle pdb=" C ALA A 855 " pdb=" CA ALA A 855 " pdb=" CB ALA A 855 " ideal model delta sigma weight residual 109.64 137.87 -28.23 1.77e+00 3.19e-01 2.54e+02 angle pdb=" N VAL A 51 " pdb=" CA VAL A 51 " pdb=" C VAL A 51 " ideal model delta sigma weight residual 108.17 123.43 -15.26 1.40e+00 5.10e-01 1.19e+02 angle pdb=" C LEU A 562 " pdb=" N PRO A 563 " pdb=" CA PRO A 563 " ideal model delta sigma weight residual 120.03 111.29 8.74 9.90e-01 1.02e+00 7.79e+01 angle pdb=" C18 B12 A1202 " pdb=" C19 B12 A1202 " pdb=" N24 B12 A1202 " ideal model delta sigma weight residual 120.00 94.26 25.74 3.00e+00 1.11e-01 7.36e+01 ... (remaining 9044 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.20: 3828 29.20 - 58.41: 191 58.41 - 87.61: 22 87.61 - 116.81: 1 116.81 - 146.02: 2 Dihedral angle restraints: 4044 sinusoidal: 1642 harmonic: 2402 Sorted by residual: dihedral pdb=" C ARG A 839 " pdb=" N ARG A 839 " pdb=" CA ARG A 839 " pdb=" CB ARG A 839 " ideal model delta harmonic sigma weight residual -122.60 -142.45 19.85 0 2.50e+00 1.60e-01 6.30e+01 dihedral pdb=" C ALA A 855 " pdb=" N ALA A 855 " pdb=" CA ALA A 855 " pdb=" CB ALA A 855 " ideal model delta harmonic sigma weight residual -122.60 -139.40 16.80 0 2.50e+00 1.60e-01 4.51e+01 dihedral pdb=" C3R B12 A1202 " pdb=" O2 B12 A1202 " pdb=" P B12 A1202 " pdb=" O4 B12 A1202 " ideal model delta sinusoidal sigma weight residual 60.00 -153.98 -146.02 1 2.00e+01 2.50e-03 4.39e+01 ... (remaining 4041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.110: 1034 1.110 - 2.220: 2 2.220 - 3.330: 2 3.330 - 4.441: 0 4.441 - 5.551: 1 Chirality restraints: 1039 Sorted by residual: chirality pdb=" C12 B12 A1202 " pdb=" C11 B12 A1202 " pdb=" C46 B12 A1202 " pdb=" C47 B12 A1202 " both_signs ideal model delta sigma weight residual False -2.64 2.91 -5.55 2.00e-01 2.50e+01 7.70e+02 chirality pdb=" N21 B12 A1202 " pdb=" C1 B12 A1202 " pdb=" C4 B12 A1202 " pdb="CO B12 A1202 " both_signs ideal model delta sigma weight residual False -3.05 0.08 -3.13 2.00e-01 2.50e+01 2.44e+02 chirality pdb=" N22 B12 A1202 " pdb=" C6 B12 A1202 " pdb=" C9 B12 A1202 " pdb="CO B12 A1202 " both_signs ideal model delta sigma weight residual False -2.93 -0.18 -2.75 2.00e-01 2.50e+01 1.89e+02 ... (remaining 1036 not shown) Planarity restraints: 1180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C35 B12 A1202 " -0.186 2.00e-02 2.50e+03 1.40e-01 2.94e+02 pdb=" C4 B12 A1202 " 0.093 2.00e-02 2.50e+03 pdb=" C5 B12 A1202 " 0.145 2.00e-02 2.50e+03 pdb=" C6 B12 A1202 " 0.038 2.00e-02 2.50e+03 pdb=" C7 B12 A1202 " 0.110 2.00e-02 2.50e+03 pdb=" N22 B12 A1202 " -0.200 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1R B12 A1202 " 0.040 2.00e-02 2.50e+03 9.59e-02 2.76e+02 pdb=" C2B B12 A1202 " -0.137 2.00e-02 2.50e+03 pdb=" C4B B12 A1202 " -0.016 2.00e-02 2.50e+03 pdb=" C5B B12 A1202 " 0.036 2.00e-02 2.50e+03 pdb=" C5M B12 A1202 " 0.094 2.00e-02 2.50e+03 pdb=" C6B B12 A1202 " 0.060 2.00e-02 2.50e+03 pdb=" C6M B12 A1202 " -0.230 2.00e-02 2.50e+03 pdb=" C7B B12 A1202 " 0.088 2.00e-02 2.50e+03 pdb=" C8B B12 A1202 " 0.072 2.00e-02 2.50e+03 pdb=" C9B B12 A1202 " -0.006 2.00e-02 2.50e+03 pdb=" N1B B12 A1202 " 0.070 2.00e-02 2.50e+03 pdb=" N3B B12 A1202 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 B12 A1202 " 0.110 2.00e-02 2.50e+03 1.60e-01 2.55e+02 pdb=" C18 B12 A1202 " 0.094 2.00e-02 2.50e+03 pdb=" C19 B12 A1202 " -0.275 2.00e-02 2.50e+03 pdb=" N24 B12 A1202 " 0.071 2.00e-02 2.50e+03 ... (remaining 1177 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 685 2.76 - 3.30: 7181 3.30 - 3.83: 10965 3.83 - 4.37: 14137 4.37 - 4.90: 22386 Nonbonded interactions: 55354 Sorted by model distance: nonbonded pdb=" N ALA A 855 " pdb=" O ALA A 855 " model vdw 2.228 2.496 nonbonded pdb=" N GLY A 321 " pdb=" O GLY A 321 " model vdw 2.275 2.496 nonbonded pdb=" N MET A 803 " pdb=" O MET A 803 " model vdw 2.375 2.496 nonbonded pdb=" N ARG A 559 " pdb=" N GLU A 560 " model vdw 2.393 2.560 nonbonded pdb=" C TYR A 854 " pdb=" C ALA A 855 " model vdw 2.394 2.800 ... (remaining 55349 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 group one per residue 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: 4.080 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: 11.810 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 22.570 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5129 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 : 0.016 0.225 6659 Z= 1.030 Angle : 2.317 28.234 9049 Z= 1.409 Chirality : 0.258 5.551 1039 Planarity : 0.017 0.160 1180 Dihedral : 17.251 146.016 2506 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 4.37 % Allowed : 14.61 % Favored : 81.02 % Cbeta Deviations : 1.17 % Peptide Plane: Cis-proline : 0.00 % 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: -4.03 (0.24), residues: 839 helix: -2.85 (0.19), residues: 387 sheet: -1.65 (0.76), residues: 47 loop : -2.56 (0.28), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.013 TRP A 166 HIS 0.013 0.004 HIS A 759 PHE 0.096 0.018 PHE A 52 TYR 0.091 0.013 TYR A 854 ARG 0.013 0.001 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 145 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 LEU cc_start: 0.5203 (mt) cc_final: 0.5002 (mt) REVERT: A 276 ARG cc_start: 0.4509 (mtm110) cc_final: 0.4093 (mmm160) REVERT: A 367 SER cc_start: 0.6095 (OUTLIER) cc_final: 0.5842 (t) REVERT: A 405 GLU cc_start: 0.6565 (OUTLIER) cc_final: 0.6037 (tt0) REVERT: A 464 ASN cc_start: 0.5844 (m-40) cc_final: 0.5216 (t0) REVERT: A 789 MET cc_start: 0.6153 (ttt) cc_final: 0.5770 (ttm) REVERT: A 820 TYR cc_start: 0.5858 (OUTLIER) cc_final: 0.3795 (p90) REVERT: A 865 MET cc_start: 0.3583 (mmm) cc_final: 0.3373 (mmt) outliers start: 29 outliers final: 6 residues processed: 168 average time/residue: 0.2438 time to fit residues: 50.6305 Evaluate side-chains 103 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 94 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain A residue 786 ILE Chi-restraints excluded: chain A residue 820 TYR Chi-restraints excluded: chain A residue 848 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 8.9990 chunk 63 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 42 optimal weight: 0.0370 chunk 34 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN A 198 GLN ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 772 ASN ** A 817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5311 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 6659 Z= 0.300 Angle : 1.131 31.063 9049 Z= 0.495 Chirality : 0.092 2.351 1039 Planarity : 0.006 0.053 1180 Dihedral : 11.856 137.246 982 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 5.27 % Allowed : 16.57 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.38 (0.26), residues: 839 helix: -1.22 (0.23), residues: 385 sheet: -1.83 (0.65), residues: 65 loop : -1.82 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 166 HIS 0.009 0.002 HIS A 759 PHE 0.019 0.002 PHE A 52 TYR 0.021 0.002 TYR A 820 ARG 0.007 0.001 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 107 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.3291 (OUTLIER) cc_final: 0.2144 (tt0) REVERT: A 81 VAL cc_start: 0.5728 (OUTLIER) cc_final: 0.5507 (t) REVERT: A 276 ARG cc_start: 0.5061 (mtm110) cc_final: 0.4174 (mmt180) REVERT: A 513 MET cc_start: 0.2479 (ptp) cc_final: 0.2220 (ptm) REVERT: A 669 ARG cc_start: 0.3932 (mtt90) cc_final: 0.3524 (mtt90) REVERT: A 707 VAL cc_start: 0.6012 (OUTLIER) cc_final: 0.5788 (t) REVERT: A 786 ILE cc_start: 0.6502 (mm) cc_final: 0.6229 (pt) REVERT: A 789 MET cc_start: 0.6080 (ttt) cc_final: 0.5830 (ttm) REVERT: A 820 TYR cc_start: 0.6728 (OUTLIER) cc_final: 0.4561 (p90) outliers start: 35 outliers final: 17 residues processed: 132 average time/residue: 0.1812 time to fit residues: 32.2469 Evaluate side-chains 108 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 87 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 820 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 chunk 63 optimal weight: 0.0170 chunk 51 optimal weight: 0.9980 chunk 21 optimal weight: 0.0970 chunk 76 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 75 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5304 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6659 Z= 0.249 Angle : 1.052 30.724 9049 Z= 0.443 Chirality : 0.091 2.410 1039 Planarity : 0.005 0.060 1180 Dihedral : 10.907 136.429 977 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.92 % Allowed : 19.43 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.82 (0.27), residues: 839 helix: -0.69 (0.24), residues: 384 sheet: -1.81 (0.63), residues: 70 loop : -1.54 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 166 HIS 0.007 0.001 HIS A 759 PHE 0.019 0.002 PHE A 643 TYR 0.017 0.002 TYR A 820 ARG 0.007 0.001 ARG A 384 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 96 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.7041 (mmt) cc_final: 0.6482 (mmt) REVERT: A 258 THR cc_start: 0.4766 (OUTLIER) cc_final: 0.4473 (p) REVERT: A 276 ARG cc_start: 0.4884 (mtm110) cc_final: 0.4069 (mmt180) REVERT: A 783 LYS cc_start: 0.6978 (OUTLIER) cc_final: 0.6771 (mtmm) REVERT: A 786 ILE cc_start: 0.6511 (mm) cc_final: 0.6304 (pt) REVERT: A 820 TYR cc_start: 0.6919 (OUTLIER) cc_final: 0.4753 (p90) outliers start: 26 outliers final: 14 residues processed: 111 average time/residue: 0.1792 time to fit residues: 27.3548 Evaluate side-chains 102 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 85 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 820 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 72 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 272 GLN ** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5485 moved from start: 0.4654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6659 Z= 0.302 Angle : 1.070 31.530 9049 Z= 0.453 Chirality : 0.092 2.385 1039 Planarity : 0.006 0.060 1180 Dihedral : 10.710 132.362 976 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 20.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 5.12 % Allowed : 20.63 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.87 (0.27), residues: 839 helix: -0.74 (0.24), residues: 387 sheet: -2.11 (0.64), residues: 62 loop : -1.52 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 166 HIS 0.015 0.003 HIS A 799 PHE 0.014 0.002 PHE A 643 TYR 0.018 0.002 TYR A 854 ARG 0.005 0.001 ARG A 384 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 98 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 ASN cc_start: 0.6403 (OUTLIER) cc_final: 0.5516 (t0) REVERT: A 610 LEU cc_start: 0.6468 (pt) cc_final: 0.5970 (mt) REVERT: A 783 LYS cc_start: 0.7105 (OUTLIER) cc_final: 0.6877 (mtmm) REVERT: A 820 TYR cc_start: 0.7193 (OUTLIER) cc_final: 0.5261 (p90) outliers start: 34 outliers final: 18 residues processed: 119 average time/residue: 0.1609 time to fit residues: 26.7034 Evaluate side-chains 109 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 88 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 820 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 1 optimal weight: 0.5980 chunk 60 optimal weight: 0.4980 chunk 33 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 0 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5464 moved from start: 0.5035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6659 Z= 0.263 Angle : 1.034 31.412 9049 Z= 0.430 Chirality : 0.090 2.390 1039 Planarity : 0.005 0.062 1180 Dihedral : 10.473 130.749 976 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 19.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 4.07 % Allowed : 22.89 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.74 (0.27), residues: 839 helix: -0.61 (0.24), residues: 388 sheet: -1.70 (0.63), residues: 67 loop : -1.54 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 166 HIS 0.006 0.002 HIS A 759 PHE 0.013 0.002 PHE A 643 TYR 0.014 0.002 TYR A 820 ARG 0.004 0.000 ARG A 384 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 98 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 LEU cc_start: 0.5859 (mt) cc_final: 0.5632 (mt) REVERT: A 820 TYR cc_start: 0.7173 (OUTLIER) cc_final: 0.5343 (p90) outliers start: 27 outliers final: 15 residues processed: 114 average time/residue: 0.1575 time to fit residues: 25.4139 Evaluate side-chains 104 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 88 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 820 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 67 optimal weight: 0.3980 chunk 37 optimal weight: 0.9980 chunk 6 optimal weight: 0.3980 chunk 26 optimal weight: 2.9990 chunk 42 optimal weight: 0.0470 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5447 moved from start: 0.5327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6659 Z= 0.233 Angle : 1.008 31.354 9049 Z= 0.418 Chirality : 0.089 2.393 1039 Planarity : 0.005 0.064 1180 Dihedral : 10.182 126.725 976 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 19.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 4.82 % Allowed : 23.19 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.75 (0.27), residues: 839 helix: -0.57 (0.24), residues: 387 sheet: -1.88 (0.64), residues: 68 loop : -1.56 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 166 HIS 0.006 0.001 HIS A 759 PHE 0.023 0.002 PHE A 643 TYR 0.014 0.001 TYR A 820 ARG 0.003 0.000 ARG A 268 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 96 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 LEU cc_start: 0.5853 (mt) cc_final: 0.5633 (mt) REVERT: A 610 LEU cc_start: 0.6127 (pt) cc_final: 0.5682 (mt) REVERT: A 722 LEU cc_start: 0.5540 (tt) cc_final: 0.5078 (mt) REVERT: A 820 TYR cc_start: 0.7218 (OUTLIER) cc_final: 0.5517 (p90) outliers start: 32 outliers final: 22 residues processed: 116 average time/residue: 0.1534 time to fit residues: 25.0369 Evaluate side-chains 110 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 87 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 820 TYR Chi-restraints excluded: chain A residue 841 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 0.2980 chunk 9 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 80 optimal weight: 0.1980 chunk 50 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5438 moved from start: 0.5586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6659 Z= 0.237 Angle : 1.010 31.116 9049 Z= 0.422 Chirality : 0.089 2.396 1039 Planarity : 0.005 0.065 1180 Dihedral : 10.161 124.607 976 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 19.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 4.37 % Allowed : 23.04 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.67 (0.27), residues: 839 helix: -0.51 (0.24), residues: 387 sheet: -1.97 (0.64), residues: 68 loop : -1.49 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 166 HIS 0.006 0.001 HIS A 759 PHE 0.019 0.002 PHE A 643 TYR 0.014 0.001 TYR A 820 ARG 0.004 0.000 ARG A 268 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 92 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 LEU cc_start: 0.5910 (mt) cc_final: 0.5700 (mt) REVERT: A 610 LEU cc_start: 0.6092 (pt) cc_final: 0.5656 (mt) REVERT: A 820 TYR cc_start: 0.7237 (OUTLIER) cc_final: 0.5581 (p90) REVERT: A 821 MET cc_start: 0.3329 (mtp) cc_final: 0.3100 (ttt) outliers start: 29 outliers final: 23 residues processed: 109 average time/residue: 0.1566 time to fit residues: 24.4100 Evaluate side-chains 111 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 87 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain A residue 730 GLN Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 820 TYR Chi-restraints excluded: chain A residue 841 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 chunk 40 optimal weight: 0.0870 chunk 7 optimal weight: 0.0970 chunk 63 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5407 moved from start: 0.5822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6659 Z= 0.226 Angle : 1.004 31.025 9049 Z= 0.417 Chirality : 0.089 2.401 1039 Planarity : 0.005 0.063 1180 Dihedral : 9.938 121.645 976 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 19.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 4.22 % Allowed : 23.19 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.52 (0.28), residues: 839 helix: -0.36 (0.25), residues: 386 sheet: -1.86 (0.63), residues: 73 loop : -1.42 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 166 HIS 0.006 0.001 HIS A 759 PHE 0.022 0.002 PHE A 711 TYR 0.014 0.001 TYR A 820 ARG 0.003 0.000 ARG A 384 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 89 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 LEU cc_start: 0.5950 (mt) cc_final: 0.5726 (mt) REVERT: A 610 LEU cc_start: 0.6128 (pt) cc_final: 0.5630 (mt) REVERT: A 716 MET cc_start: 0.7269 (mmm) cc_final: 0.6900 (tpt) REVERT: A 820 TYR cc_start: 0.7314 (OUTLIER) cc_final: 0.5800 (p90) outliers start: 28 outliers final: 21 residues processed: 106 average time/residue: 0.1552 time to fit residues: 23.6997 Evaluate side-chains 107 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 85 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain A residue 640 PHE Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 820 TYR Chi-restraints excluded: chain A residue 841 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 68 optimal weight: 0.0870 chunk 71 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 79 optimal weight: 0.0870 chunk 48 optimal weight: 0.5980 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5434 moved from start: 0.5921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6659 Z= 0.239 Angle : 1.018 31.194 9049 Z= 0.425 Chirality : 0.089 2.393 1039 Planarity : 0.005 0.063 1180 Dihedral : 9.919 120.759 976 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 19.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.92 % Allowed : 23.34 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.59 (0.28), residues: 839 helix: -0.47 (0.25), residues: 388 sheet: -1.77 (0.66), residues: 68 loop : -1.45 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 166 HIS 0.005 0.001 HIS A 759 PHE 0.017 0.002 PHE A 643 TYR 0.013 0.001 TYR A 820 ARG 0.003 0.000 ARG A 268 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 88 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 604 VAL cc_start: 0.8187 (p) cc_final: 0.7948 (m) REVERT: A 610 LEU cc_start: 0.6000 (pt) cc_final: 0.5591 (mt) REVERT: A 716 MET cc_start: 0.7482 (mmm) cc_final: 0.7098 (tpt) REVERT: A 820 TYR cc_start: 0.7353 (OUTLIER) cc_final: 0.6167 (p90) outliers start: 26 outliers final: 21 residues processed: 102 average time/residue: 0.1527 time to fit residues: 22.2893 Evaluate side-chains 108 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 86 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain A residue 640 PHE Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 820 TYR Chi-restraints excluded: chain A residue 841 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 0.0770 chunk 55 optimal weight: 0.9990 chunk 83 optimal weight: 0.2980 chunk 77 optimal weight: 0.0870 chunk 66 optimal weight: 0.9980 chunk 6 optimal weight: 0.0770 chunk 51 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 70 optimal weight: 0.2980 chunk 20 optimal weight: 0.7980 overall best weight: 0.1674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5292 moved from start: 0.6110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6659 Z= 0.189 Angle : 0.985 30.815 9049 Z= 0.408 Chirality : 0.088 2.415 1039 Planarity : 0.005 0.064 1180 Dihedral : 9.506 117.368 976 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.86 % Allowed : 24.40 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.28), residues: 839 helix: -0.26 (0.25), residues: 395 sheet: -1.42 (0.62), residues: 78 loop : -1.49 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 166 HIS 0.006 0.001 HIS A 759 PHE 0.018 0.001 PHE A 643 TYR 0.012 0.001 TYR A 820 ARG 0.003 0.000 ARG A 384 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 89 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.7143 (mmt) cc_final: 0.6919 (mmt) REVERT: A 210 MET cc_start: 0.3013 (mtt) cc_final: 0.2449 (mtp) REVERT: A 604 VAL cc_start: 0.8284 (p) cc_final: 0.8060 (m) REVERT: A 814 MET cc_start: 0.4723 (tpt) cc_final: 0.4385 (tpt) REVERT: A 820 TYR cc_start: 0.7313 (OUTLIER) cc_final: 0.5981 (p90) outliers start: 19 outliers final: 18 residues processed: 101 average time/residue: 0.1486 time to fit residues: 21.5666 Evaluate side-chains 102 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 83 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain A residue 640 PHE Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain A residue 820 TYR Chi-restraints excluded: chain A residue 841 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 68 optimal weight: 0.0980 chunk 8 optimal weight: 0.2980 chunk 12 optimal weight: 0.0970 chunk 58 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4858 r_free = 0.4858 target = 0.233968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.216807 restraints weight = 8360.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.218645 restraints weight = 6620.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.220722 restraints weight = 5127.045| |-----------------------------------------------------------------------------| r_work (final): 0.4738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5457 moved from start: 0.6199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6659 Z= 0.225 Angle : 1.014 31.033 9049 Z= 0.420 Chirality : 0.088 2.398 1039 Planarity : 0.005 0.063 1180 Dihedral : 9.595 117.748 976 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.86 % Allowed : 25.15 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.28), residues: 839 helix: -0.28 (0.25), residues: 395 sheet: -1.65 (0.66), residues: 68 loop : -1.43 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 166 HIS 0.005 0.001 HIS A 521 PHE 0.016 0.001 PHE A 643 TYR 0.013 0.001 TYR A 820 ARG 0.003 0.000 ARG A 268 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1683.61 seconds wall clock time: 31 minutes 16.16 seconds (1876.16 seconds total)