Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 17:47:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f4u_31454/04_2023/7f4u_31454.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f4u_31454/04_2023/7f4u_31454.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f4u_31454/04_2023/7f4u_31454.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f4u_31454/04_2023/7f4u_31454.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f4u_31454/04_2023/7f4u_31454.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f4u_31454/04_2023/7f4u_31454.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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 34 5.16 5 C 5059 2.51 5 N 1476 2.21 5 O 1510 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 9": "NH1" <-> "NH2" Residue "A GLU 14": "OE1" <-> "OE2" Residue "A PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 33": "OE1" <-> "OE2" Residue "A ARG 37": "NH1" <-> "NH2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 50": "OE1" <-> "OE2" Residue "A ARG 64": "NH1" <-> "NH2" Residue "A ARG 69": "NH1" <-> "NH2" Residue "A GLU 76": "OE1" <-> "OE2" Residue "A GLU 85": "OE1" <-> "OE2" Residue "A PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 116": "NH1" <-> "NH2" Residue "A ARG 122": "NH1" <-> "NH2" Residue "A ARG 126": "NH1" <-> "NH2" Residue "A GLU 138": "OE1" <-> "OE2" Residue "A ARG 142": "NH1" <-> "NH2" Residue "A ARG 170": "NH1" <-> "NH2" Residue "A GLU 174": "OE1" <-> "OE2" Residue "A PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 186": "NH1" <-> "NH2" Residue "A GLU 190": "OE1" <-> "OE2" Residue "A ARG 194": "NH1" <-> "NH2" Residue "A ASP 201": "OD1" <-> "OD2" Residue "A ARG 226": "NH1" <-> "NH2" Residue "A GLU 229": "OE1" <-> "OE2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A ARG 250": "NH1" <-> "NH2" Residue "A ARG 254": "NH1" <-> "NH2" Residue "A ARG 283": "NH1" <-> "NH2" Residue "A ARG 309": "NH1" <-> "NH2" Residue "A ARG 329": "NH1" <-> "NH2" Residue "A GLU 341": "OE1" <-> "OE2" Residue "A ARG 358": "NH1" <-> "NH2" Residue "A ARG 377": "NH1" <-> "NH2" Residue "A ARG 380": "NH1" <-> "NH2" Residue "A ARG 394": "NH1" <-> "NH2" Residue "A ASP 396": "OD1" <-> "OD2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A ARG 416": "NH1" <-> "NH2" Residue "A TYR 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 431": "OD1" <-> "OD2" Residue "A GLU 432": "OE1" <-> "OE2" Residue "B PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 372": "OD1" <-> "OD2" Residue "B ASP 393": "OD1" <-> "OD2" Residue "B ASP 394": "OD1" <-> "OD2" Residue "B GLU 437": "OE1" <-> "OE2" Residue "B TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 506": "OD1" <-> "OD2" Residue "B GLU 510": "OE1" <-> "OE2" Residue "B GLU 563": "OE1" <-> "OE2" Residue "B ASP 662": "OD1" <-> "OD2" Residue "B TYR 697": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 8079 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3416 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 415} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 4178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 4178 Classifications: {'peptide': 690} Incomplete info: {'truncation_to_alanine': 408} Link IDs: {'PTRANS': 12, 'TRANS': 677} Chain breaks: 10 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 1112 Unresolved non-hydrogen angles: 1520 Unresolved non-hydrogen dihedrals: 776 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 6, 'ASN:plan1': 5, 'TYR:plan': 4, 'UNK:plan-1': 226, 'TRP:plan': 4, 'ASP:plan': 14, 'PHE:plan': 7, 'GLU:plan': 20, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 579 Chain: "C" Number of atoms: 485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 485 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'TRANS': 96} Chain breaks: 5 Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 291 Unresolved non-hydrogen dihedrals: 97 Planarities with less than four sites: {'UNK:plan-1': 97} Unresolved non-hydrogen planarities: 97 Time building chain proxies: 5.05, per 1000 atoms: 0.63 Number of scatterers: 8079 At special positions: 0 Unit cell: (78.11, 121.98, 189.39, 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 34 16.00 O 1510 8.00 N 1476 7.00 C 5059 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: 3.79 Conformation dependent library (CDL) restraints added in 1.3 seconds 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2364 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 0 sheets defined 105.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 7 through 21 Processing helix chain 'A' and resid 24 through 38 Processing helix chain 'A' and resid 48 through 56 Processing helix chain 'A' and resid 58 through 68 Processing helix chain 'A' and resid 73 through 78 removed outlier: 3.957A pdb=" N LEU A 78 " --> pdb=" O TRP A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 93 removed outlier: 3.564A pdb=" N PHE A 91 " --> pdb=" O TRP A 87 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 110 removed outlier: 4.442A pdb=" N PHE A 100 " --> pdb=" O ALA A 96 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU A 101 " --> pdb=" O ASP A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 130 removed outlier: 3.602A pdb=" N GLU A 130 " --> pdb=" O ARG A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 140 removed outlier: 4.423A pdb=" N GLN A 140 " --> pdb=" O MET A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 167 removed outlier: 6.424A pdb=" N VAL A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL A 161 " --> pdb=" O LEU A 157 " (cutoff:3.500A) Proline residue: A 164 - end of helix removed outlier: 3.968A pdb=" N LEU A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 176 Processing helix chain 'A' and resid 183 through 203 removed outlier: 4.074A pdb=" N LEU A 203 " --> pdb=" O VAL A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 225 removed outlier: 3.560A pdb=" N LYS A 220 " --> pdb=" O GLN A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 243 Proline residue: A 236 - end of helix removed outlier: 4.323A pdb=" N GLN A 243 " --> pdb=" O ALA A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 258 removed outlier: 3.506A pdb=" N GLN A 258 " --> pdb=" O ARG A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 274 Processing helix chain 'A' and resid 277 through 286 removed outlier: 3.966A pdb=" N GLY A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 306 Processing helix chain 'A' and resid 313 through 326 Processing helix chain 'A' and resid 331 through 349 Processing helix chain 'A' and resid 353 through 370 removed outlier: 4.440A pdb=" N GLN A 370 " --> pdb=" O ILE A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 395 removed outlier: 4.072A pdb=" N CYS A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LEU A 395 " --> pdb=" O VAL A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 416 removed outlier: 4.053A pdb=" N ARG A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 430 removed outlier: 3.544A pdb=" N LYS A 425 " --> pdb=" O GLY A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 449 Processing helix chain 'B' and resid 167 through 185 Processing helix chain 'B' and resid 193 through 197 Processing helix chain 'B' and resid 198 through 208 removed outlier: 3.813A pdb=" N UNK B 202 " --> pdb=" O UNK B 198 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N UNK B 208 " --> pdb=" O UNK B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 222 removed outlier: 3.536A pdb=" N UNK B 216 " --> pdb=" O UNK B 213 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N UNK B 217 " --> pdb=" O UNK B 214 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N UNK B 222 " --> pdb=" O UNK B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 261 removed outlier: 4.687A pdb=" N ASP B 249 " --> pdb=" O PHE B 245 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N GLU B 250 " --> pdb=" O ILE B 246 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN B 251 " --> pdb=" O MET B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 280 removed outlier: 3.998A pdb=" N ALA B 269 " --> pdb=" O GLU B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 301 Processing helix chain 'B' and resid 302 through 305 Processing helix chain 'B' and resid 309 through 325 removed outlier: 3.525A pdb=" N LEU B 318 " --> pdb=" O VAL B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 341 removed outlier: 3.819A pdb=" N ALA B 335 " --> pdb=" O PRO B 331 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL B 337 " --> pdb=" O LEU B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 359 Processing helix chain 'B' and resid 368 through 385 removed outlier: 3.602A pdb=" N ASP B 372 " --> pdb=" O LYS B 368 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B 381 " --> pdb=" O SER B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 390 removed outlier: 3.797A pdb=" N ASN B 390 " --> pdb=" O PRO B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 411 removed outlier: 3.674A pdb=" N THR B 400 " --> pdb=" O GLY B 396 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B 411 " --> pdb=" O TYR B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 420 Processing helix chain 'B' and resid 421 through 436 removed outlier: 3.864A pdb=" N GLN B 434 " --> pdb=" O LYS B 430 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 436 " --> pdb=" O LEU B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 495 removed outlier: 3.987A pdb=" N LEU B 487 " --> pdb=" O ARG B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 515 removed outlier: 3.537A pdb=" N LEU B 511 " --> pdb=" O HIS B 507 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N SER B 515 " --> pdb=" O LEU B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 535 removed outlier: 3.697A pdb=" N ALA B 522 " --> pdb=" O TYR B 518 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY B 535 " --> pdb=" O THR B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 568 Processing helix chain 'B' and resid 617 through 641 Processing helix chain 'B' and resid 643 through 647 removed outlier: 3.760A pdb=" N CYS B 646 " --> pdb=" O LYS B 643 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU B 647 " --> pdb=" O ASP B 644 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 643 through 647' Processing helix chain 'B' and resid 648 through 660 removed outlier: 3.657A pdb=" N ALA B 652 " --> pdb=" O LEU B 648 " (cutoff:3.500A) Proline residue: B 655 - end of helix Processing helix chain 'B' and resid 665 through 683 Processing helix chain 'B' and resid 687 through 693 removed outlier: 3.642A pdb=" N ILE B 691 " --> pdb=" O LEU B 687 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN B 692 " --> pdb=" O GLN B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 695 through 708 Processing helix chain 'B' and resid 715 through 723 removed outlier: 4.281A pdb=" N LEU B 719 " --> pdb=" O THR B 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 727 through 729 No H-bonds generated for 'chain 'B' and resid 727 through 729' Processing helix chain 'B' and resid 730 through 748 removed outlier: 5.027A pdb=" N ASP B 736 " --> pdb=" O PRO B 732 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL B 737 " --> pdb=" O LEU B 733 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU B 745 " --> pdb=" O VAL B 741 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP B 746 " --> pdb=" O LEU B 742 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N PHE B 748 " --> pdb=" O THR B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 771 removed outlier: 3.736A pdb=" N VAL B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 858 through 873 Processing helix chain 'B' and resid 878 through 892 removed outlier: 4.064A pdb=" N UNK B 882 " --> pdb=" O UNK B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 898 through 915 Processing helix chain 'B' and resid 924 through 935 Processing helix chain 'B' and resid 939 through 954 Processing helix chain 'B' and resid 978 through 991 removed outlier: 4.492A pdb=" N UNK B 990 " --> pdb=" O UNK B 986 " (cutoff:3.500A) Processing helix chain 'B' and resid 995 through 1003 removed outlier: 3.800A pdb=" N UNK B 999 " --> pdb=" O UNK B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1028 Processing helix chain 'B' and resid 1046 through 1051 removed outlier: 3.510A pdb=" N UNK B1051 " --> pdb=" O UNK B1047 " (cutoff:3.500A) Processing helix chain 'B' and resid 1059 through 1067 Processing helix chain 'B' and resid 1068 through 1070 No H-bonds generated for 'chain 'B' and resid 1068 through 1070' Processing helix chain 'C' and resid 42 through 48 removed outlier: 4.769A pdb=" N UNK C 47 " --> pdb=" O UNK C 43 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N UNK C 48 " --> pdb=" O UNK C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 76 removed outlier: 4.543A pdb=" N UNK C 76 " --> pdb=" O UNK C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 111 Processing helix chain 'C' and resid 122 through 131 Processing helix chain 'C' and resid 144 through 163 Processing helix chain 'C' and resid 177 through 188 removed outlier: 4.750A pdb=" N UNK C 186 " --> pdb=" O UNK C 182 " (cutoff:3.500A) 596 hydrogen bonds defined for protein. 1764 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: 2.37 Time building geometry restraints manager: 4.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2841 1.34 - 1.46: 1508 1.46 - 1.58: 3756 1.58 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 8159 Sorted by residual: bond pdb=" N ASP B 540 " pdb=" CA ASP B 540 " ideal model delta sigma weight residual 1.455 1.482 -0.027 1.21e-02 6.83e+03 5.07e+00 bond pdb=" N GLU B 539 " pdb=" CA GLU B 539 " ideal model delta sigma weight residual 1.457 1.482 -0.025 1.29e-02 6.01e+03 3.65e+00 bond pdb=" CA ASP B 540 " pdb=" CB ASP B 540 " ideal model delta sigma weight residual 1.533 1.509 0.024 1.72e-02 3.38e+03 1.95e+00 bond pdb=" CA VAL B 306 " pdb=" CB VAL B 306 " ideal model delta sigma weight residual 1.540 1.521 0.019 1.36e-02 5.41e+03 1.95e+00 bond pdb=" C PRO A 400 " pdb=" N PRO A 401 " ideal model delta sigma weight residual 1.334 1.366 -0.032 2.34e-02 1.83e+03 1.91e+00 ... (remaining 8154 not shown) Histogram of bond angle deviations from ideal: 100.46 - 107.20: 188 107.20 - 113.94: 4770 113.94 - 120.67: 3442 120.67 - 127.41: 2693 127.41 - 134.15: 53 Bond angle restraints: 11146 Sorted by residual: angle pdb=" N PRO B 331 " pdb=" CA PRO B 331 " pdb=" CB PRO B 331 " ideal model delta sigma weight residual 103.46 110.27 -6.81 9.30e-01 1.16e+00 5.36e+01 angle pdb=" N PRO B 302 " pdb=" CA PRO B 302 " pdb=" CB PRO B 302 " ideal model delta sigma weight residual 103.51 110.24 -6.73 9.60e-01 1.09e+00 4.91e+01 angle pdb=" N PRO B 345 " pdb=" CA PRO B 345 " pdb=" CB PRO B 345 " ideal model delta sigma weight residual 103.25 110.49 -7.24 1.05e+00 9.07e-01 4.75e+01 angle pdb=" N PRO B 262 " pdb=" CA PRO B 262 " pdb=" CB PRO B 262 " ideal model delta sigma weight residual 103.25 110.23 -6.98 1.05e+00 9.07e-01 4.42e+01 angle pdb=" N PRO B 732 " pdb=" CA PRO B 732 " pdb=" CB PRO B 732 " ideal model delta sigma weight residual 103.39 110.17 -6.78 1.08e+00 8.57e-01 3.94e+01 ... (remaining 11141 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4521 17.95 - 35.90: 343 35.90 - 53.85: 56 53.85 - 71.80: 16 71.80 - 89.75: 6 Dihedral angle restraints: 4942 sinusoidal: 1355 harmonic: 3587 Sorted by residual: dihedral pdb=" CA VAL B 364 " pdb=" C VAL B 364 " pdb=" N VAL B 365 " pdb=" CA VAL B 365 " ideal model delta harmonic sigma weight residual 180.00 145.58 34.42 0 5.00e+00 4.00e-02 4.74e+01 dihedral pdb=" CA PHE A 180 " pdb=" C PHE A 180 " pdb=" N PRO A 181 " pdb=" CA PRO A 181 " ideal model delta harmonic sigma weight residual 180.00 145.60 34.40 0 5.00e+00 4.00e-02 4.73e+01 dihedral pdb=" CA LYS B 281 " pdb=" C LYS B 281 " pdb=" N LYS B 282 " pdb=" CA LYS B 282 " ideal model delta harmonic sigma weight residual 180.00 150.13 29.87 0 5.00e+00 4.00e-02 3.57e+01 ... (remaining 4939 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1136 0.051 - 0.101: 247 0.101 - 0.152: 24 0.152 - 0.203: 0 0.203 - 0.254: 6 Chirality restraints: 1413 Sorted by residual: chirality pdb=" CA PRO B 331 " pdb=" N PRO B 331 " pdb=" C PRO B 331 " pdb=" CB PRO B 331 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA PRO B 302 " pdb=" N PRO B 302 " pdb=" C PRO B 302 " pdb=" CB PRO B 302 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA PRO B 772 " pdb=" N PRO B 772 " pdb=" C PRO B 772 " pdb=" CB PRO B 772 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 1410 not shown) Planarity restraints: 1469 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 180 " 0.064 5.00e-02 4.00e+02 9.64e-02 1.49e+01 pdb=" N PRO A 181 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO A 181 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 181 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 385 " -0.041 5.00e-02 4.00e+02 6.18e-02 6.11e+00 pdb=" N PRO B 386 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO B 386 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 386 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 400 " -0.033 5.00e-02 4.00e+02 4.99e-02 3.99e+00 pdb=" N PRO A 401 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 401 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 401 " -0.028 5.00e-02 4.00e+02 ... (remaining 1466 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 133 2.65 - 3.21: 8929 3.21 - 3.77: 12493 3.77 - 4.34: 15878 4.34 - 4.90: 23816 Nonbonded interactions: 61249 Sorted by model distance: nonbonded pdb=" O SER A 346 " pdb=" ND1 HIS A 351 " model vdw 2.087 2.520 nonbonded pdb=" O GLU B 568 " pdb=" NZ LYS B 659 " model vdw 2.135 2.520 nonbonded pdb=" O VAL A 199 " pdb=" OG SER A 202 " model vdw 2.174 2.440 nonbonded pdb=" O LEU A 133 " pdb=" N VAL A 135 " model vdw 2.201 2.520 nonbonded pdb=" O ARG A 358 " pdb=" OG SER A 361 " model vdw 2.214 2.440 ... (remaining 61244 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: 3.000 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: 0.000 Extract box with map and model: 9.310 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 25.480 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6152 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 8159 Z= 0.245 Angle : 0.874 9.382 11146 Z= 0.493 Chirality : 0.042 0.254 1413 Planarity : 0.005 0.096 1469 Dihedral : 14.593 89.746 2578 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 18.07 Ramachandran Plot: Outliers : 0.56 % Allowed : 14.38 % Favored : 85.06 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.12 % 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: -5.17 (0.21), residues: 890 helix: -2.52 (0.17), residues: 613 sheet: None (None), residues: 0 loop : -5.38 (0.23), residues: 277 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.2272 time to fit residues: 78.8158 Evaluate side-chains 242 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 0.841 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN A 228 GLN A 258 GLN A 356 GLN A 370 GLN A 427 GLN B 352 ASN B 513 HIS B 626 GLN B 630 GLN B 663 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6136 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 8159 Z= 0.255 Angle : 0.793 10.298 11146 Z= 0.395 Chirality : 0.040 0.183 1413 Planarity : 0.006 0.096 1469 Dihedral : 5.758 33.936 1264 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 19.31 Ramachandran Plot: Outliers : 0.11 % Allowed : 15.39 % Favored : 84.49 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.12 % 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: -3.34 (0.25), residues: 890 helix: -1.08 (0.19), residues: 623 sheet: None (None), residues: 0 loop : -4.96 (0.29), residues: 267 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 254 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 254 average time/residue: 0.2403 time to fit residues: 78.7457 Evaluate side-chains 236 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 235 time to evaluate : 0.821 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1092 time to fit residues: 1.3794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 26 optimal weight: 0.2980 chunk 14 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 13 optimal weight: 0.0970 chunk 48 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 GLN ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 GLN ** A 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 513 HIS ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 626 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6140 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 8159 Z= 0.266 Angle : 0.794 9.677 11146 Z= 0.398 Chirality : 0.040 0.173 1413 Planarity : 0.006 0.096 1469 Dihedral : 5.624 32.994 1264 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.34 % Allowed : 13.71 % Favored : 85.96 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.12 % 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: -2.63 (0.26), residues: 890 helix: -0.56 (0.19), residues: 631 sheet: None (None), residues: 0 loop : -4.76 (0.31), residues: 259 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 246 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 246 average time/residue: 0.2388 time to fit residues: 75.9109 Evaluate side-chains 235 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 233 time to evaluate : 0.804 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1139 time to fit residues: 1.4987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 47 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 GLN ** B 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 513 HIS B 630 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6107 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 8159 Z= 0.236 Angle : 0.773 8.307 11146 Z= 0.386 Chirality : 0.040 0.152 1413 Planarity : 0.005 0.092 1469 Dihedral : 5.402 33.528 1264 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.22 % Allowed : 14.16 % Favored : 85.62 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.11 (0.27), residues: 890 helix: -0.12 (0.20), residues: 627 sheet: None (None), residues: 0 loop : -4.67 (0.31), residues: 263 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 252 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 252 average time/residue: 0.2369 time to fit residues: 76.9312 Evaluate side-chains 239 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 238 time to evaluate : 0.855 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1077 time to fit residues: 1.3401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 ASN ** A 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 379 HIS ** B 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 513 HIS ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 GLN ** B 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6156 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 8159 Z= 0.284 Angle : 0.815 9.251 11146 Z= 0.407 Chirality : 0.040 0.205 1413 Planarity : 0.006 0.101 1469 Dihedral : 5.526 33.282 1264 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 18.20 Ramachandran Plot: Outliers : 0.22 % Allowed : 14.94 % Favored : 84.83 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.07 (0.27), residues: 890 helix: -0.01 (0.20), residues: 619 sheet: None (None), residues: 0 loop : -4.74 (0.30), residues: 271 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.2403 time to fit residues: 75.7332 Evaluate side-chains 236 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 0.848 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 10 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 23 optimal weight: 0.0970 chunk 4 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 GLN A 258 GLN A 292 ASN A 357 GLN ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 513 HIS ** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6082 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 8159 Z= 0.221 Angle : 0.766 8.084 11146 Z= 0.377 Chirality : 0.039 0.167 1413 Planarity : 0.005 0.089 1469 Dihedral : 5.293 31.900 1264 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.22 % Allowed : 13.82 % Favored : 85.96 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.88 (0.28), residues: 890 helix: 0.12 (0.20), residues: 632 sheet: None (None), residues: 0 loop : -4.85 (0.31), residues: 258 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 250 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 251 average time/residue: 0.2328 time to fit residues: 75.9182 Evaluate side-chains 240 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 239 time to evaluate : 0.902 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1096 time to fit residues: 1.3359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 51 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 20 optimal weight: 0.4980 chunk 30 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 ASN ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 513 HIS ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6131 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 8159 Z= 0.264 Angle : 0.813 9.018 11146 Z= 0.405 Chirality : 0.041 0.176 1413 Planarity : 0.005 0.082 1469 Dihedral : 5.484 32.639 1264 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 19.30 Ramachandran Plot: Outliers : 0.22 % Allowed : 14.83 % Favored : 84.94 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.98 (0.27), residues: 890 helix: 0.02 (0.20), residues: 630 sheet: None (None), residues: 0 loop : -4.80 (0.31), residues: 260 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.2397 time to fit residues: 74.1689 Evaluate side-chains 232 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 0.752 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 9 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 28 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 224 HIS A 292 ASN ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 513 HIS ** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 626 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6054 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 8159 Z= 0.220 Angle : 0.807 10.838 11146 Z= 0.393 Chirality : 0.040 0.157 1413 Planarity : 0.006 0.088 1469 Dihedral : 5.303 31.183 1264 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.22 % Allowed : 12.81 % Favored : 86.97 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.70 (0.28), residues: 890 helix: 0.28 (0.20), residues: 627 sheet: None (None), residues: 0 loop : -4.75 (0.31), residues: 263 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.2318 time to fit residues: 73.3694 Evaluate side-chains 232 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 0.844 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 20 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 43 optimal weight: 0.0970 chunk 45 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 31 optimal weight: 0.5980 chunk 50 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 chunk 23 optimal weight: 0.0040 chunk 34 optimal weight: 0.3980 overall best weight: 0.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 513 HIS ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 689 HIS ** B 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5986 moved from start: 0.4469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 8159 Z= 0.201 Angle : 0.771 9.307 11146 Z= 0.375 Chirality : 0.038 0.158 1413 Planarity : 0.006 0.115 1469 Dihedral : 5.077 29.706 1264 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.22 % Allowed : 12.81 % Favored : 86.97 % Rotamer Outliers : 0.00 % 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: -1.40 (0.28), residues: 890 helix: 0.49 (0.20), residues: 628 sheet: None (None), residues: 0 loop : -4.63 (0.32), residues: 262 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 247 average time/residue: 0.2391 time to fit residues: 76.3483 Evaluate side-chains 234 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 0.850 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 52 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 42 optimal weight: 0.0670 chunk 4 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 12 optimal weight: 0.1980 chunk 38 optimal weight: 0.2980 chunk 6 optimal weight: 2.9990 overall best weight: 0.5120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 HIS ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 513 HIS ** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 689 HIS B 693 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6005 moved from start: 0.4595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 8159 Z= 0.217 Angle : 0.777 9.076 11146 Z= 0.381 Chirality : 0.039 0.173 1413 Planarity : 0.006 0.120 1469 Dihedral : 5.080 30.812 1264 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.22 % Allowed : 13.15 % Favored : 86.63 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.28), residues: 890 helix: 0.46 (0.20), residues: 630 sheet: None (None), residues: 0 loop : -4.63 (0.33), residues: 260 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.2461 time to fit residues: 76.8293 Evaluate side-chains 231 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 0.801 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 11 optimal weight: 2.9990 chunk 42 optimal weight: 0.0270 chunk 17 optimal weight: 1.9990 chunk 43 optimal weight: 0.0070 chunk 5 optimal weight: 0.1980 chunk 7 optimal weight: 1.9990 chunk 36 optimal weight: 0.0470 chunk 2 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.2354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 513 HIS B 689 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.124759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.099393 restraints weight = 22118.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.102165 restraints weight = 15880.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.104226 restraints weight = 12176.417| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.4954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 8159 Z= 0.203 Angle : 0.788 9.209 11146 Z= 0.377 Chirality : 0.039 0.162 1413 Planarity : 0.006 0.116 1469 Dihedral : 4.967 29.785 1264 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.22 % Allowed : 11.12 % Favored : 88.65 % Rotamer Outliers : 0.00 % 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: -1.24 (0.29), residues: 890 helix: 0.60 (0.21), residues: 634 sheet: None (None), residues: 0 loop : -4.65 (0.32), residues: 256 =============================================================================== Job complete usr+sys time: 2121.26 seconds wall clock time: 38 minutes 44.37 seconds (2324.37 seconds total)