Starting phenix.real_space_refine (version: 1.21rc1) on Sat Aug 12 07:03:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hm0_34887/08_2023/8hm0_34887.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hm0_34887/08_2023/8hm0_34887.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hm0_34887/08_2023/8hm0_34887.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hm0_34887/08_2023/8hm0_34887.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hm0_34887/08_2023/8hm0_34887.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hm0_34887/08_2023/8hm0_34887.pdb" } resolution = 3.1 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= 0.003 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 60 5.16 5 C 7219 2.51 5 N 1915 2.21 5 O 2137 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 12": "OE1" <-> "OE2" Residue "C GLU 365": "OE1" <-> "OE2" Residue "A GLU 14": "OE1" <-> "OE2" Residue "A GLU 28": "OE1" <-> "OE2" Residue "A GLU 93": "OE1" <-> "OE2" Residue "A GLU 106": "OE1" <-> "OE2" Residue "A PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 229": "OE1" <-> "OE2" Residue "A GLU 253": "OE1" <-> "OE2" Residue "A GLU 293": "OE1" <-> "OE2" Residue "A GLU 339": "OE1" <-> "OE2" Residue "A GLU 476": "OE1" <-> "OE2" Residue "A GLU 633": "OE1" <-> "OE2" Residue "A GLU 758": "OE1" <-> "OE2" Residue "A GLU 769": "OE1" <-> "OE2" Residue "A GLU 775": "OE1" <-> "OE2" Residue "A GLU 822": "OE1" <-> "OE2" Residue "A GLU 830": "OE1" <-> "OE2" Residue "A GLU 852": "OE1" <-> "OE2" Residue "A GLU 856": "OE1" <-> "OE2" Residue "A GLU 879": "OE1" <-> "OE2" Residue "A GLU 888": "OE1" <-> "OE2" Residue "A GLU 969": "OE1" <-> "OE2" Residue "A GLU 978": "OE1" <-> "OE2" Residue "B GLU 20": "OE1" <-> "OE2" Residue "B GLU 32": "OE1" <-> "OE2" Residue "B GLU 41": "OE1" <-> "OE2" Residue "B GLU 80": "OE1" <-> "OE2" Residue "B GLU 91": "OE1" <-> "OE2" Residue "B GLU 171": "OE1" <-> "OE2" Residue "B GLU 190": "OE1" <-> "OE2" Residue "B GLU 203": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 11331 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 1996 Classifications: {'peptide': 323} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 185} Link IDs: {'PTRANS': 6, 'TRANS': 316} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 675 Unresolved non-hydrogen angles: 854 Unresolved non-hydrogen dihedrals: 558 Unresolved non-hydrogen chiralities: 60 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 8, 'ASN:plan1': 12, 'TRP:plan': 1, 'ASP:plan': 18, 'PHE:plan': 14, 'GLU:plan': 15, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 371 Chain: "A" Number of atoms: 7592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 935, 7592 Classifications: {'peptide': 935} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 31, 'TRANS': 900} Chain breaks: 3 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1743 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 202} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 6.28, per 1000 atoms: 0.55 Number of scatterers: 11331 At special positions: 0 Unit cell: (100.768, 121.136, 136.144, 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 60 16.00 O 2137 8.00 N 1915 7.00 C 7219 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: 4.74 Conformation dependent library (CDL) restraints added in 1.8 seconds 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2828 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 14 sheets defined 34.9% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'C' and resid 3 through 19 removed outlier: 3.628A pdb=" N ASN C 9 " --> pdb=" O ALA C 5 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER C 19 " --> pdb=" O SER C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 23 Processing helix chain 'C' and resid 24 through 43 removed outlier: 3.909A pdb=" N THR C 41 " --> pdb=" O TRP C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 121 removed outlier: 4.004A pdb=" N ALA C 113 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP C 119 " --> pdb=" O ASN C 115 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASP C 121 " --> pdb=" O VAL C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 159 removed outlier: 3.600A pdb=" N ILE C 151 " --> pdb=" O SER C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 188 removed outlier: 4.685A pdb=" N MET C 184 " --> pdb=" O LEU C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 321 removed outlier: 3.699A pdb=" N ASN C 321 " --> pdb=" O LYS C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 341 Processing helix chain 'C' and resid 343 through 350 removed outlier: 3.617A pdb=" N ASN C 350 " --> pdb=" O ARG C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 360 Processing helix chain 'C' and resid 367 through 373 Processing helix chain 'C' and resid 407 through 425 removed outlier: 3.615A pdb=" N THR C 416 " --> pdb=" O SER C 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 49 Processing helix chain 'A' and resid 108 through 118 removed outlier: 3.607A pdb=" N ASN A 117 " --> pdb=" O PHE A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 149 removed outlier: 3.736A pdb=" N PHE A 149 " --> pdb=" O PRO A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 209 through 220 Processing helix chain 'A' and resid 240 through 253 Processing helix chain 'A' and resid 267 through 281 Processing helix chain 'A' and resid 330 through 339 Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 380 through 389 Processing helix chain 'A' and resid 439 through 445 removed outlier: 3.737A pdb=" N LYS A 445 " --> pdb=" O ALA A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 473 removed outlier: 3.898A pdb=" N CYS A 466 " --> pdb=" O ASP A 462 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLN A 467 " --> pdb=" O ALA A 463 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TRP A 470 " --> pdb=" O CYS A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 486 removed outlier: 3.881A pdb=" N ASP A 480 " --> pdb=" O GLU A 476 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA A 484 " --> pdb=" O ASP A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 502 Processing helix chain 'A' and resid 502 through 511 removed outlier: 3.544A pdb=" N LEU A 511 " --> pdb=" O LEU A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 561 Processing helix chain 'A' and resid 579 through 590 Processing helix chain 'A' and resid 621 through 643 Processing helix chain 'A' and resid 648 through 666 removed outlier: 3.724A pdb=" N ASP A 654 " --> pdb=" O LYS A 650 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER A 666 " --> pdb=" O ILE A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 672 removed outlier: 3.797A pdb=" N GLY A 672 " --> pdb=" O TYR A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 701 removed outlier: 3.613A pdb=" N SER A 689 " --> pdb=" O LYS A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 776 removed outlier: 3.678A pdb=" N ARG A 776 " --> pdb=" O LYS A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 847 Processing helix chain 'A' and resid 859 through 883 removed outlier: 3.655A pdb=" N ARG A 883 " --> pdb=" O GLU A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 979 removed outlier: 3.898A pdb=" N THR A 976 " --> pdb=" O PHE A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 996 Processing helix chain 'B' and resid 19 through 38 removed outlier: 4.519A pdb=" N SER B 24 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N GLN B 25 " --> pdb=" O PRO B 21 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 26 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU B 28 " --> pdb=" O SER B 24 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL B 33 " --> pdb=" O PHE B 29 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N SER B 35 " --> pdb=" O ASN B 31 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N TRP B 36 " --> pdb=" O GLU B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 55 Processing helix chain 'B' and resid 87 through 96 removed outlier: 3.589A pdb=" N GLU B 91 " --> pdb=" O LYS B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 150 removed outlier: 5.720A pdb=" N LYS B 139 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ILE B 140 " --> pdb=" O TYR B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 202 Processing sheet with id=AA1, first strand: chain 'C' and resid 130 through 132 Processing sheet with id=AA2, first strand: chain 'C' and resid 214 through 219 Processing sheet with id=AA3, first strand: chain 'C' and resid 226 through 229 removed outlier: 6.971A pdb=" N ILE C 232 " --> pdb=" O ILE C 228 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 375 through 380 removed outlier: 6.289A pdb=" N GLU C 380 " --> pdb=" O VAL C 384 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N VAL C 384 " --> pdb=" O GLU C 380 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 133 through 136 removed outlier: 7.043A pdb=" N CYS A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N TYR A 140 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N PHE A 31 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE A 17 " --> pdb=" O SER A 11 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ARG A 23 " --> pdb=" O CYS A 5 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N CYS A 5 " --> pdb=" O ARG A 23 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N CYS A 124 " --> pdb=" O ILE A 153 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 38 through 43 removed outlier: 6.278A pdb=" N SER A 84 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ARG A 64 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ALA A 86 " --> pdb=" O LYS A 62 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LYS A 62 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N MET A 88 " --> pdb=" O MET A 60 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 72 through 73 removed outlier: 6.780A pdb=" N ILE A 614 " --> pdb=" O VAL A 569 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL A 571 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N ILE A 612 " --> pdb=" O VAL A 571 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 166 through 169 removed outlier: 7.153A pdb=" N SER A 184 " --> pdb=" O ASN A 204 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE A 200 " --> pdb=" O TYR A 188 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU A 222 " --> pdb=" O LEU A 238 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 258 through 259 Processing sheet with id=AB1, first strand: chain 'A' and resid 285 through 287 Processing sheet with id=AB2, first strand: chain 'A' and resid 300 through 302 removed outlier: 3.523A pdb=" N THR A 317 " --> pdb=" O ARG A 302 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 355 through 364 removed outlier: 6.931A pdb=" N THR A 369 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ARG A 363 " --> pdb=" O GLU A 367 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLU A 367 " --> pdb=" O ARG A 363 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG A 407 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ILE A 401 " --> pdb=" O VAL A 397 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 745 through 748 removed outlier: 3.649A pdb=" N GLU A 758 " --> pdb=" O ARG A 746 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL A 748 " --> pdb=" O PHE A 756 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N PHE A 756 " --> pdb=" O VAL A 748 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE A 548 " --> pdb=" O VAL A 755 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER A 812 " --> pdb=" O ALA A 793 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 116 through 119 removed outlier: 6.625A pdb=" N VAL B 62 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TRP B 119 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N VAL B 64 " --> pdb=" O TRP B 119 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N CYS B 63 " --> pdb=" O TYR B 156 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N LEU B 155 " --> pdb=" O ILE B 177 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 412 hydrogen bonds defined for protein. 1185 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: 3.62 Time building geometry restraints manager: 4.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3691 1.34 - 1.46: 2284 1.46 - 1.58: 5489 1.58 - 1.69: 0 1.69 - 1.81: 89 Bond restraints: 11553 Sorted by residual: bond pdb=" C GLU B 20 " pdb=" N PRO B 21 " ideal model delta sigma weight residual 1.336 1.367 -0.031 1.08e-02 8.57e+03 8.26e+00 bond pdb=" CG LEU A 563 " pdb=" CD1 LEU A 563 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.63e+00 bond pdb=" CA ASP A 373 " pdb=" C ASP A 373 " ideal model delta sigma weight residual 1.523 1.508 0.015 1.21e-02 6.83e+03 1.54e+00 bond pdb=" CA SER A 708 " pdb=" C SER A 708 " ideal model delta sigma weight residual 1.532 1.521 0.012 9.60e-03 1.09e+04 1.45e+00 bond pdb=" N VAL B 64 " pdb=" CA VAL B 64 " ideal model delta sigma weight residual 1.474 1.456 0.018 1.57e-02 4.06e+03 1.35e+00 ... (remaining 11548 not shown) Histogram of bond angle deviations from ideal: 99.71 - 106.58: 262 106.58 - 113.46: 6297 113.46 - 120.34: 4335 120.34 - 127.22: 4684 127.22 - 134.10: 82 Bond angle restraints: 15660 Sorted by residual: angle pdb=" N THR C 41 " pdb=" CA THR C 41 " pdb=" C THR C 41 " ideal model delta sigma weight residual 114.56 109.83 4.73 1.27e+00 6.20e-01 1.39e+01 angle pdb=" N SER A 780 " pdb=" CA SER A 780 " pdb=" C SER A 780 " ideal model delta sigma weight residual 114.64 109.00 5.64 1.52e+00 4.33e-01 1.38e+01 angle pdb=" C ILE A 609 " pdb=" N SER A 610 " pdb=" CA SER A 610 " ideal model delta sigma weight residual 122.56 117.62 4.94 1.50e+00 4.44e-01 1.08e+01 angle pdb=" C PRO A 721 " pdb=" N PHE A 722 " pdb=" CA PHE A 722 " ideal model delta sigma weight residual 121.54 127.59 -6.05 1.91e+00 2.74e-01 1.00e+01 angle pdb=" N THR A 752 " pdb=" CA THR A 752 " pdb=" C THR A 752 " ideal model delta sigma weight residual 114.62 111.03 3.59 1.14e+00 7.69e-01 9.92e+00 ... (remaining 15655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 6049 17.88 - 35.77: 701 35.77 - 53.65: 179 53.65 - 71.54: 39 71.54 - 89.42: 17 Dihedral angle restraints: 6985 sinusoidal: 2624 harmonic: 4361 Sorted by residual: dihedral pdb=" CA GLY A 434 " pdb=" C GLY A 434 " pdb=" N LYS A 435 " pdb=" CA LYS A 435 " ideal model delta harmonic sigma weight residual 180.00 151.72 28.28 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA GLU C 365 " pdb=" C GLU C 365 " pdb=" N ALA C 366 " pdb=" CA ALA C 366 " ideal model delta harmonic sigma weight residual -180.00 -152.22 -27.78 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA SER B 153 " pdb=" C SER B 153 " pdb=" N VAL B 154 " pdb=" CA VAL B 154 " ideal model delta harmonic sigma weight residual 180.00 154.12 25.88 0 5.00e+00 4.00e-02 2.68e+01 ... (remaining 6982 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 972 0.031 - 0.062: 544 0.062 - 0.093: 177 0.093 - 0.125: 72 0.125 - 0.156: 15 Chirality restraints: 1780 Sorted by residual: chirality pdb=" CA ASP A 400 " pdb=" N ASP A 400 " pdb=" C ASP A 400 " pdb=" CB ASP A 400 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.05e-01 chirality pdb=" CB ILE A 739 " pdb=" CA ILE A 739 " pdb=" CG1 ILE A 739 " pdb=" CG2 ILE A 739 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.99e-01 chirality pdb=" CB VAL B 178 " pdb=" CA VAL B 178 " pdb=" CG1 VAL B 178 " pdb=" CG2 VAL B 178 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.55e-01 ... (remaining 1777 not shown) Planarity restraints: 2015 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 554 " -0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO A 555 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 555 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 555 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 593 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.83e+00 pdb=" N PRO A 594 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 594 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 594 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 564 " -0.028 5.00e-02 4.00e+02 4.15e-02 2.75e+00 pdb=" N PRO A 565 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 565 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 565 " -0.023 5.00e-02 4.00e+02 ... (remaining 2012 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 558 2.71 - 3.26: 11439 3.26 - 3.80: 17513 3.80 - 4.35: 22258 4.35 - 4.90: 37335 Nonbonded interactions: 89103 Sorted by model distance: nonbonded pdb=" N ASP A 439 " pdb=" OD1 ASP A 439 " model vdw 2.162 2.520 nonbonded pdb=" O ALA C 5 " pdb=" OG1 THR C 8 " model vdw 2.213 2.440 nonbonded pdb=" O LYS A 973 " pdb=" OG SER A 977 " model vdw 2.220 2.440 nonbonded pdb=" NH1 ARG A 23 " pdb=" OG1 THR A 29 " model vdw 2.224 2.520 nonbonded pdb=" OE2 GLU A 205 " pdb=" NH1 ARG A 223 " model vdw 2.244 2.520 ... (remaining 89098 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 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: 4.830 Check model and map are aligned: 0.180 Set scattering table: 0.100 Process input model: 32.770 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 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 : 0.005 0.042 11553 Z= 0.309 Angle : 0.724 8.729 15660 Z= 0.433 Chirality : 0.044 0.156 1780 Planarity : 0.004 0.045 2015 Dihedral : 17.210 89.420 4157 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.82 % Favored : 90.11 % Rotamer Outliers : 9.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.07 % 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: -4.58 (0.18), residues: 1456 helix: -2.64 (0.18), residues: 498 sheet: -2.41 (0.33), residues: 212 loop : -3.60 (0.19), residues: 746 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 162 time to evaluate : 1.452 Fit side-chains revert: symmetry clash outliers start: 116 outliers final: 85 residues processed: 266 average time/residue: 0.2389 time to fit residues: 90.1882 Evaluate side-chains 225 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 140 time to evaluate : 1.424 Switching outliers to nearest non-outliers outliers start: 85 outliers final: 0 residues processed: 85 average time/residue: 0.1157 time to fit residues: 19.6179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 37 optimal weight: 0.0040 chunk 74 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 chunk 114 optimal weight: 5.9990 chunk 44 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 overall best weight: 1.0596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN A 524 GLN A 562 ASN A 576 ASN A 730 ASN A 839 HIS A 860 ASN B 25 GLN B 55 GLN B 59 ASN B 111 ASN B 146 GLN B 188 GLN B 214 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 11553 Z= 0.236 Angle : 0.620 8.674 15660 Z= 0.330 Chirality : 0.044 0.187 1780 Planarity : 0.004 0.045 2015 Dihedral : 5.383 31.134 1599 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer Outliers : 4.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.39 (0.20), residues: 1456 helix: -1.35 (0.21), residues: 514 sheet: -2.10 (0.32), residues: 225 loop : -3.03 (0.21), residues: 717 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 154 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 21 residues processed: 195 average time/residue: 0.2618 time to fit residues: 71.5823 Evaluate side-chains 157 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 136 time to evaluate : 1.552 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1376 time to fit residues: 6.8539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 73 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 132 optimal weight: 0.7980 chunk 143 optimal weight: 4.9990 chunk 118 optimal weight: 9.9990 chunk 131 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 106 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 GLN A 860 ASN A 994 GLN B 214 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 11553 Z= 0.187 Angle : 0.575 7.775 15660 Z= 0.305 Chirality : 0.043 0.154 1780 Planarity : 0.004 0.052 2015 Dihedral : 5.072 28.829 1599 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer Outliers : 3.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.07 % 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: -2.78 (0.21), residues: 1456 helix: -0.72 (0.22), residues: 514 sheet: -1.96 (0.32), residues: 231 loop : -2.69 (0.22), residues: 711 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 160 time to evaluate : 1.376 Fit side-chains revert: symmetry clash outliers start: 46 outliers final: 19 residues processed: 193 average time/residue: 0.2556 time to fit residues: 69.4836 Evaluate side-chains 161 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 142 time to evaluate : 1.306 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1320 time to fit residues: 6.1634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 131 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 14 optimal weight: 0.0030 chunk 63 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 133 optimal weight: 0.8980 chunk 141 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 386 ASN ** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 ASN ** A 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 860 ASN B 188 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 11553 Z= 0.241 Angle : 0.593 7.801 15660 Z= 0.312 Chirality : 0.044 0.151 1780 Planarity : 0.004 0.036 2015 Dihedral : 4.991 27.215 1599 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer Outliers : 2.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.07 % 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: -2.56 (0.21), residues: 1456 helix: -0.60 (0.22), residues: 523 sheet: -1.67 (0.33), residues: 219 loop : -2.60 (0.22), residues: 714 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 143 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 15 residues processed: 172 average time/residue: 0.2564 time to fit residues: 62.4447 Evaluate side-chains 148 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 133 time to evaluate : 1.364 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1081 time to fit residues: 4.8902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 117 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 120 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 860 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 11553 Z= 0.297 Angle : 0.609 7.854 15660 Z= 0.321 Chirality : 0.045 0.184 1780 Planarity : 0.004 0.037 2015 Dihedral : 5.062 27.541 1599 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer Outliers : 2.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.07 % 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: -2.48 (0.21), residues: 1456 helix: -0.55 (0.22), residues: 526 sheet: -1.55 (0.34), residues: 208 loop : -2.56 (0.22), residues: 722 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 142 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 15 residues processed: 164 average time/residue: 0.2499 time to fit residues: 58.1266 Evaluate side-chains 151 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 136 time to evaluate : 1.468 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1174 time to fit residues: 5.5025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 141 optimal weight: 0.6980 chunk 117 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 chunk 11 optimal weight: 9.9990 chunk 46 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 11553 Z= 0.186 Angle : 0.571 8.409 15660 Z= 0.301 Chirality : 0.043 0.142 1780 Planarity : 0.004 0.037 2015 Dihedral : 4.849 26.152 1599 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer Outliers : 1.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.07 % 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: -2.17 (0.21), residues: 1456 helix: -0.22 (0.23), residues: 513 sheet: -1.43 (0.34), residues: 208 loop : -2.40 (0.22), residues: 735 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 148 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 7 residues processed: 161 average time/residue: 0.2684 time to fit residues: 60.9362 Evaluate side-chains 144 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 137 time to evaluate : 1.373 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1139 time to fit residues: 3.3553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 136 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 80 optimal weight: 0.3980 chunk 103 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 118 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 140 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 85 optimal weight: 0.3980 chunk 64 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 11553 Z= 0.199 Angle : 0.574 8.406 15660 Z= 0.302 Chirality : 0.044 0.148 1780 Planarity : 0.004 0.037 2015 Dihedral : 4.823 27.997 1599 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer Outliers : 1.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.07 % 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: -2.03 (0.21), residues: 1456 helix: -0.09 (0.23), residues: 514 sheet: -1.34 (0.34), residues: 208 loop : -2.33 (0.22), residues: 734 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 146 time to evaluate : 1.515 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 11 residues processed: 161 average time/residue: 0.2667 time to fit residues: 61.0040 Evaluate side-chains 157 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 146 time to evaluate : 1.507 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1133 time to fit residues: 4.3547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 87 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 42 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 13 optimal weight: 30.0000 chunk 110 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 11553 Z= 0.259 Angle : 0.608 7.774 15660 Z= 0.318 Chirality : 0.045 0.158 1780 Planarity : 0.004 0.037 2015 Dihedral : 4.937 31.331 1599 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer Outliers : 1.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.01 (0.21), residues: 1456 helix: -0.08 (0.23), residues: 513 sheet: -1.40 (0.33), residues: 218 loop : -2.29 (0.22), residues: 725 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 149 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 15 residues processed: 163 average time/residue: 0.2516 time to fit residues: 58.3780 Evaluate side-chains 157 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 142 time to evaluate : 1.434 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1120 time to fit residues: 5.0053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 134 optimal weight: 0.0970 chunk 122 optimal weight: 8.9990 chunk 131 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 102 optimal weight: 0.0970 chunk 40 optimal weight: 3.9990 chunk 118 optimal weight: 6.9990 chunk 124 optimal weight: 0.4980 chunk 130 optimal weight: 1.9990 chunk 86 optimal weight: 0.0970 overall best weight: 0.2974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 11553 Z= 0.141 Angle : 0.560 7.255 15660 Z= 0.295 Chirality : 0.043 0.161 1780 Planarity : 0.004 0.037 2015 Dihedral : 4.681 28.187 1599 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer Outliers : 0.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.07 % 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: -1.72 (0.22), residues: 1456 helix: 0.21 (0.23), residues: 506 sheet: -1.22 (0.34), residues: 214 loop : -2.14 (0.22), residues: 736 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 164 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 167 average time/residue: 0.2432 time to fit residues: 58.5100 Evaluate side-chains 153 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 149 time to evaluate : 1.402 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1186 time to fit residues: 2.9016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 138 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 133 optimal weight: 8.9990 chunk 115 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 11553 Z= 0.241 Angle : 0.604 8.831 15660 Z= 0.317 Chirality : 0.045 0.174 1780 Planarity : 0.004 0.038 2015 Dihedral : 4.819 25.885 1599 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer Outliers : 0.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.07 % 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: -1.77 (0.22), residues: 1456 helix: 0.08 (0.23), residues: 515 sheet: -1.24 (0.34), residues: 215 loop : -2.12 (0.22), residues: 726 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 150 time to evaluate : 1.448 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 154 average time/residue: 0.2477 time to fit residues: 54.7315 Evaluate side-chains 148 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 144 time to evaluate : 1.406 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1174 time to fit residues: 2.8586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 32 optimal weight: 0.7980 chunk 116 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 14 optimal weight: 0.0980 chunk 21 optimal weight: 6.9990 chunk 101 optimal weight: 7.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 426 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 = 0.4327 r_free = 0.4327 target = 0.179251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.125913 restraints weight = 16539.295| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.42 r_work: 0.3493 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 11553 Z= 0.269 Angle : 0.633 10.157 15660 Z= 0.331 Chirality : 0.045 0.213 1780 Planarity : 0.004 0.038 2015 Dihedral : 4.881 27.108 1599 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.07 % 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: -1.79 (0.21), residues: 1456 helix: 0.06 (0.23), residues: 517 sheet: -1.22 (0.34), residues: 214 loop : -2.15 (0.22), residues: 725 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2884.22 seconds wall clock time: 52 minutes 55.69 seconds (3175.69 seconds total)