Starting phenix.real_space_refine on Sat Jul 20 10:22:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gub_34272/07_2024/8gub_34272_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gub_34272/07_2024/8gub_34272.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gub_34272/07_2024/8gub_34272.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gub_34272/07_2024/8gub_34272.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gub_34272/07_2024/8gub_34272_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gub_34272/07_2024/8gub_34272_trim.cif" } resolution = 2.73 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= 0.051 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: 5 Type Number sf(0) Gaussians S 73 5.16 5 C 6594 2.51 5 N 1790 2.21 5 O 1898 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 76": "OE1" <-> "OE2" Residue "A PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 538": "OD1" <-> "OD2" Residue "A GLU 674": "OE1" <-> "OE2" Residue "A PHE 794": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 915": "OD1" <-> "OD2" Residue "A TYR 988": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 10358 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 977, 7998 Classifications: {'peptide': 977} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 931} Chain breaks: 4 Chain: "B" Number of atoms: 2330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2330 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 271} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'1LT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.56, per 1000 atoms: 0.54 Number of scatterers: 10358 At special positions: 0 Unit cell: (87.822, 119.952, 119.952, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 73 16.00 F 3 9.00 O 1898 8.00 N 1790 7.00 C 6594 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: 3.85 Conformation dependent library (CDL) restraints added in 1.8 seconds 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2400 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 13 sheets defined 51.6% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 41 through 54 removed outlier: 3.606A pdb=" N PHE A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS A 51 " --> pdb=" O HIS A 47 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU A 52 " --> pdb=" O GLU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 93 removed outlier: 3.866A pdb=" N ARG A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 122 Processing helix chain 'A' and resid 125 through 131 removed outlier: 3.797A pdb=" N ASP A 129 " --> pdb=" O VAL A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 143 Processing helix chain 'A' and resid 143 through 155 removed outlier: 3.656A pdb=" N ASP A 155 " --> pdb=" O VAL A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 167 Processing helix chain 'A' and resid 178 through 183 removed outlier: 3.569A pdb=" N ASN A 183 " --> pdb=" O LYS A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 229 removed outlier: 3.944A pdb=" N ARG A 226 " --> pdb=" O ALA A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 280 Processing helix chain 'A' and resid 290 through 295 Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.919A pdb=" N ARG A 309 " --> pdb=" O PRO A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 330 No H-bonds generated for 'chain 'A' and resid 328 through 330' Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 488 through 499 Processing helix chain 'A' and resid 527 through 536 removed outlier: 3.703A pdb=" N LEU A 531 " --> pdb=" O ASP A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 554 Processing helix chain 'A' and resid 555 through 558 Processing helix chain 'A' and resid 561 through 563 No H-bonds generated for 'chain 'A' and resid 561 through 563' Processing helix chain 'A' and resid 564 through 571 removed outlier: 3.697A pdb=" N LEU A 570 " --> pdb=" O PRO A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 588 removed outlier: 3.604A pdb=" N GLN A 582 " --> pdb=" O ASP A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 599 Processing helix chain 'A' and resid 600 through 603 removed outlier: 3.555A pdb=" N ASP A 603 " --> pdb=" O GLU A 600 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 600 through 603' Processing helix chain 'A' and resid 608 through 623 Processing helix chain 'A' and resid 624 through 631 Processing helix chain 'A' and resid 631 through 638 Processing helix chain 'A' and resid 647 through 658 Processing helix chain 'A' and resid 660 through 674 removed outlier: 3.511A pdb=" N PHE A 666 " --> pdb=" O ARG A 662 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU A 674 " --> pdb=" O HIS A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 695 removed outlier: 3.671A pdb=" N ALA A 694 " --> pdb=" O SER A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 722 removed outlier: 4.186A pdb=" N HIS A 701 " --> pdb=" O MET A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 741 Processing helix chain 'A' and resid 741 through 748 removed outlier: 3.592A pdb=" N ALA A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 828 Processing helix chain 'A' and resid 857 through 864 Processing helix chain 'A' and resid 875 through 885 removed outlier: 3.643A pdb=" N ASN A 885 " --> pdb=" O LEU A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 911 removed outlier: 4.214A pdb=" N ALA A 892 " --> pdb=" O GLU A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 945 removed outlier: 4.026A pdb=" N PHE A 945 " --> pdb=" O LYS A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 965 Processing helix chain 'A' and resid 974 through 994 removed outlier: 3.736A pdb=" N ARG A 979 " --> pdb=" O ARG A 975 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS A 994 " --> pdb=" O ALA A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1004 removed outlier: 3.613A pdb=" N PHE A 998 " --> pdb=" O HIS A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1009 removed outlier: 3.945A pdb=" N GLY A1009 " --> pdb=" O LEU A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1020 removed outlier: 3.738A pdb=" N ILE A1019 " --> pdb=" O SER A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1026 Processing helix chain 'A' and resid 1031 through 1050 Processing helix chain 'B' and resid 339 through 347 removed outlier: 3.557A pdb=" N GLU B 345 " --> pdb=" O GLU B 341 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS B 346 " --> pdb=" O GLU B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 removed outlier: 4.079A pdb=" N GLY B 388 " --> pdb=" O HIS B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 409 Processing helix chain 'B' and resid 412 through 416 removed outlier: 3.549A pdb=" N GLN B 415 " --> pdb=" O SER B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 435 removed outlier: 3.789A pdb=" N GLN B 433 " --> pdb=" O SER B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 506 Processing helix chain 'B' and resid 518 through 584 removed outlier: 3.574A pdb=" N ILE B 524 " --> pdb=" O GLU B 520 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N MET B 525 " --> pdb=" O ILE B 521 " (cutoff:3.500A) Proline residue: B 568 - end of helix removed outlier: 3.509A pdb=" N GLN B 572 " --> pdb=" O PRO B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 597 removed outlier: 3.853A pdb=" N ASN B 595 " --> pdb=" O LYS B 592 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 36 removed outlier: 3.721A pdb=" N MET A 30 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N LEU A 99 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N GLU A 23 " --> pdb=" O LEU A 99 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 70 through 73 removed outlier: 4.496A pdb=" N PHE A 70 " --> pdb=" O PHE A 82 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A 72 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 203 through 212 removed outlier: 6.559A pdb=" N ASP A 203 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL A 198 " --> pdb=" O ASP A 203 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ILE A 197 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ALA A 289 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 13.928A pdb=" N SER A 199 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU A 252 " --> pdb=" O PHE A 261 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 324 through 326 Processing sheet with id=AA5, first strand: chain 'A' and resid 382 through 392 removed outlier: 6.653A pdb=" N TRP A 383 " --> pdb=" O CYS A 340 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N CYS A 340 " --> pdb=" O TRP A 383 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU A 334 " --> pdb=" O TYR A 389 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ILE A 338 " --> pdb=" O GLU A 476 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N GLU A 476 " --> pdb=" O ILE A 338 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N CYS A 340 " --> pdb=" O GLU A 474 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 371 through 372 Processing sheet with id=AA7, first strand: chain 'A' and resid 371 through 372 removed outlier: 3.608A pdb=" N LYS A 353 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU A 404 " --> pdb=" O TRP A 424 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N TRP A 424 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE A 406 " --> pdb=" O LEU A 422 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 3.778A pdb=" N GLU A 365 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 430 through 431 removed outlier: 3.526A pdb=" N THR A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 751 through 752 Processing sheet with id=AB2, first strand: chain 'A' and resid 770 through 771 Processing sheet with id=AB3, first strand: chain 'A' and resid 854 through 856 Processing sheet with id=AB4, first strand: chain 'B' and resid 377 through 381 removed outlier: 4.180A pdb=" N THR B 354 " --> pdb=" O ARG B 373 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE B 355 " --> pdb=" O TYR B 426 " (cutoff:3.500A) 497 hydrogen bonds defined for protein. 1437 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: 3.22 Time building geometry restraints manager: 4.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1736 1.30 - 1.43: 2686 1.43 - 1.55: 6035 1.55 - 1.68: 6 1.68 - 1.81: 112 Bond restraints: 10575 Sorted by residual: bond pdb=" C9 1LT A1101 " pdb=" S 1LT A1101 " ideal model delta sigma weight residual 1.738 1.521 0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C2 1LT A1101 " pdb=" S 1LT A1101 " ideal model delta sigma weight residual 1.734 1.521 0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" N 1LT A1101 " pdb=" C1 1LT A1101 " ideal model delta sigma weight residual 1.368 1.566 -0.198 2.00e-02 2.50e+03 9.77e+01 bond pdb=" C5 1LT A1101 " pdb=" C6 1LT A1101 " ideal model delta sigma weight residual 1.525 1.351 0.174 2.00e-02 2.50e+03 7.56e+01 bond pdb=" N 1LT A1101 " pdb=" C2 1LT A1101 " ideal model delta sigma weight residual 1.291 1.415 -0.124 2.00e-02 2.50e+03 3.85e+01 ... (remaining 10570 not shown) Histogram of bond angle deviations from ideal: 99.78 - 106.72: 277 106.72 - 113.66: 5970 113.66 - 120.60: 4428 120.60 - 127.53: 3479 127.53 - 134.47: 110 Bond angle restraints: 14264 Sorted by residual: angle pdb=" C2 1LT A1101 " pdb=" S 1LT A1101 " pdb=" C9 1LT A1101 " ideal model delta sigma weight residual 88.90 107.32 -18.42 3.00e+00 1.11e-01 3.77e+01 angle pdb=" N1 1LT A1101 " pdb=" C2 1LT A1101 " pdb=" S 1LT A1101 " ideal model delta sigma weight residual 118.47 134.47 -16.00 3.00e+00 1.11e-01 2.85e+01 angle pdb=" C CYS A 971 " pdb=" N THR A 972 " pdb=" CA THR A 972 " ideal model delta sigma weight residual 120.28 127.27 -6.99 1.34e+00 5.57e-01 2.72e+01 angle pdb=" N 1LT A1101 " pdb=" C2 1LT A1101 " pdb=" N1 1LT A1101 " ideal model delta sigma weight residual 126.74 117.02 9.72 3.00e+00 1.11e-01 1.05e+01 angle pdb=" N 1LT A1101 " pdb=" C1 1LT A1101 " pdb=" C9 1LT A1101 " ideal model delta sigma weight residual 115.40 108.21 7.19 3.00e+00 1.11e-01 5.75e+00 ... (remaining 14259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 5769 17.67 - 35.34: 584 35.34 - 53.01: 95 53.01 - 70.67: 12 70.67 - 88.34: 16 Dihedral angle restraints: 6476 sinusoidal: 2777 harmonic: 3699 Sorted by residual: dihedral pdb=" CA MET A 922 " pdb=" C MET A 922 " pdb=" N VAL A 923 " pdb=" CA VAL A 923 " ideal model delta harmonic sigma weight residual 180.00 -161.21 -18.79 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA GLN B 591 " pdb=" C GLN B 591 " pdb=" N LYS B 592 " pdb=" CA LYS B 592 " ideal model delta harmonic sigma weight residual 180.00 161.76 18.24 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA ASP A 258 " pdb=" C ASP A 258 " pdb=" N GLU A 259 " pdb=" CA GLU A 259 " ideal model delta harmonic sigma weight residual 180.00 162.21 17.79 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 6473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 806 0.028 - 0.056: 482 0.056 - 0.084: 162 0.084 - 0.111: 65 0.111 - 0.139: 23 Chirality restraints: 1538 Sorted by residual: chirality pdb=" CG LEU A 793 " pdb=" CB LEU A 793 " pdb=" CD1 LEU A 793 " pdb=" CD2 LEU A 793 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CA PRO A 562 " pdb=" N PRO A 562 " pdb=" C PRO A 562 " pdb=" CB PRO A 562 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" CA ASN A 918 " pdb=" N ASN A 918 " pdb=" C ASN A 918 " pdb=" CB ASN A 918 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.41e-01 ... (remaining 1535 not shown) Planarity restraints: 1832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 103 " -0.024 5.00e-02 4.00e+02 3.73e-02 2.23e+00 pdb=" N PRO A 104 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 104 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 104 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 538 " 0.023 5.00e-02 4.00e+02 3.48e-02 1.94e+00 pdb=" N PRO A 539 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 539 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 539 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 158 " 0.023 5.00e-02 4.00e+02 3.42e-02 1.87e+00 pdb=" N PRO A 159 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 159 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 159 " 0.019 5.00e-02 4.00e+02 ... (remaining 1829 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.58: 124 2.58 - 3.16: 9663 3.16 - 3.74: 15682 3.74 - 4.32: 23165 4.32 - 4.90: 37719 Nonbonded interactions: 86353 Sorted by model distance: nonbonded pdb=" NH2 ARG A 401 " pdb=" O PRO A 458 " model vdw 1.994 2.520 nonbonded pdb=" OH TYR A 584 " pdb=" OD1 ASP A 608 " model vdw 2.005 2.440 nonbonded pdb=" O SER A 292 " pdb=" NE2 GLN A 296 " model vdw 2.023 2.520 nonbonded pdb=" OG1 THR A 358 " pdb=" OH TYR A 389 " model vdw 2.055 2.440 nonbonded pdb=" N ARG A 19 " pdb=" O CYS A 36 " model vdw 2.061 2.520 ... (remaining 86348 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.300 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 27.870 Find NCS groups from input model: 0.080 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:12.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6272 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 : 0.008 0.217 10575 Z= 0.496 Angle : 0.620 18.425 14264 Z= 0.304 Chirality : 0.041 0.139 1538 Planarity : 0.003 0.037 1832 Dihedral : 14.425 88.342 4076 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 34.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.17 % Allowed : 0.35 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.24), residues: 1241 helix: 0.70 (0.22), residues: 566 sheet: -1.12 (0.41), residues: 166 loop : -0.75 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 583 HIS 0.004 0.001 HIS A 47 PHE 0.015 0.002 PHE A 667 TYR 0.009 0.001 TYR A 904 ARG 0.007 0.000 ARG A 154 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 199 time to evaluate : 1.179 Fit side-chains revert: symmetry clash REVERT: A 75 GLN cc_start: 0.7141 (mm110) cc_final: 0.6867 (mp-120) REVERT: A 76 GLU cc_start: 0.5684 (mt-10) cc_final: 0.5423 (tm-30) REVERT: A 107 ASN cc_start: 0.6180 (t0) cc_final: 0.5893 (t0) REVERT: A 127 GLU cc_start: 0.6548 (mm-30) cc_final: 0.6303 (mt-10) REVERT: A 130 MET cc_start: 0.6340 (mmm) cc_final: 0.5683 (mmp) REVERT: A 132 LYS cc_start: 0.7135 (mmtm) cc_final: 0.6858 (mptp) REVERT: A 152 ASP cc_start: 0.7107 (m-30) cc_final: 0.6630 (m-30) REVERT: A 164 MET cc_start: 0.6227 (mtt) cc_final: 0.6018 (mtm) REVERT: A 179 LYS cc_start: 0.6408 (tptp) cc_final: 0.6162 (mmmm) REVERT: A 265 TYR cc_start: 0.6397 (m-10) cc_final: 0.5975 (m-10) REVERT: A 282 MET cc_start: 0.6865 (tpp) cc_final: 0.6451 (tpp) REVERT: A 382 ARG cc_start: 0.7778 (ttm-80) cc_final: 0.7552 (ttm-80) REVERT: A 410 LYS cc_start: 0.7177 (tppp) cc_final: 0.6705 (tptp) REVERT: A 453 GLU cc_start: 0.6104 (tt0) cc_final: 0.5445 (tm-30) REVERT: A 579 GLU cc_start: 0.7432 (mm-30) cc_final: 0.6793 (mt-10) REVERT: A 583 MET cc_start: 0.6887 (tpt) cc_final: 0.6499 (tpt) REVERT: A 677 ASN cc_start: 0.7441 (t0) cc_final: 0.6877 (t0) REVERT: A 697 MET cc_start: 0.7032 (tpt) cc_final: 0.6763 (mmp) REVERT: A 732 MET cc_start: 0.6052 (tpt) cc_final: 0.5845 (mmm) REVERT: A 739 MET cc_start: 0.6661 (mtm) cc_final: 0.6424 (mtt) REVERT: A 745 MET cc_start: 0.7042 (tpt) cc_final: 0.6556 (mmm) REVERT: A 772 MET cc_start: 0.6764 (mtp) cc_final: 0.6220 (mtp) REVERT: A 777 ARG cc_start: 0.6237 (mtm110) cc_final: 0.5497 (mmm160) REVERT: A 780 TRP cc_start: 0.7439 (t-100) cc_final: 0.6913 (t-100) REVERT: A 811 MET cc_start: 0.7512 (mtp) cc_final: 0.7239 (mtm) REVERT: A 852 ARG cc_start: 0.6085 (mtm-85) cc_final: 0.5604 (mtm-85) REVERT: A 886 LYS cc_start: 0.7576 (ptpt) cc_final: 0.6687 (pttm) REVERT: A 915 ASP cc_start: 0.7000 (t70) cc_final: 0.6730 (t70) REVERT: A 933 ASP cc_start: 0.7821 (t0) cc_final: 0.6973 (t0) REVERT: A 1010 MET cc_start: 0.7254 (mtm) cc_final: 0.6945 (mtt) REVERT: A 1029 ASP cc_start: 0.7031 (m-30) cc_final: 0.6692 (m-30) REVERT: B 421 ASP cc_start: 0.7794 (t0) cc_final: 0.7383 (m-30) REVERT: B 472 ARG cc_start: 0.6037 (tmm-80) cc_final: 0.5261 (ttm170) REVERT: B 479 MET cc_start: 0.5793 (mtp) cc_final: 0.5360 (mpp) REVERT: B 520 GLU cc_start: 0.7982 (tt0) cc_final: 0.7743 (tm-30) REVERT: B 555 GLU cc_start: 0.6061 (tp30) cc_final: 0.5720 (tt0) REVERT: B 559 ILE cc_start: 0.5862 (mt) cc_final: 0.5526 (mp) outliers start: 2 outliers final: 1 residues processed: 200 average time/residue: 1.2212 time to fit residues: 262.8119 Evaluate side-chains 156 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 155 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 569 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 879 GLN ** A 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 936 HIS ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6254 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10575 Z= 0.289 Angle : 0.626 9.057 14264 Z= 0.326 Chirality : 0.046 0.264 1538 Planarity : 0.004 0.039 1832 Dihedral : 6.177 78.126 1395 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.18 % Allowed : 9.40 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.24), residues: 1241 helix: 1.41 (0.21), residues: 589 sheet: -0.62 (0.43), residues: 157 loop : -0.59 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 552 HIS 0.005 0.001 HIS A 362 PHE 0.026 0.002 PHE A 667 TYR 0.015 0.002 TYR B 470 ARG 0.005 0.001 ARG A 79 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 166 time to evaluate : 1.247 Fit side-chains revert: symmetry clash REVERT: A 75 GLN cc_start: 0.7322 (mm110) cc_final: 0.7025 (mp-120) REVERT: A 76 GLU cc_start: 0.5707 (mt-10) cc_final: 0.5349 (mm-30) REVERT: A 127 GLU cc_start: 0.6320 (mm-30) cc_final: 0.6030 (mt-10) REVERT: A 130 MET cc_start: 0.6424 (mmm) cc_final: 0.5487 (mmt) REVERT: A 152 ASP cc_start: 0.7165 (m-30) cc_final: 0.6809 (m-30) REVERT: A 179 LYS cc_start: 0.6248 (tptp) cc_final: 0.5874 (mmmm) REVERT: A 265 TYR cc_start: 0.6578 (m-10) cc_final: 0.6282 (m-10) REVERT: A 282 MET cc_start: 0.6849 (tpp) cc_final: 0.6411 (tpp) REVERT: A 384 ASN cc_start: 0.7908 (t0) cc_final: 0.6675 (m-40) REVERT: A 441 MET cc_start: 0.7660 (OUTLIER) cc_final: 0.7347 (ttm) REVERT: A 453 GLU cc_start: 0.6024 (tt0) cc_final: 0.5570 (tm-30) REVERT: A 549 ASP cc_start: 0.6071 (t0) cc_final: 0.5605 (m-30) REVERT: A 677 ASN cc_start: 0.7755 (t0) cc_final: 0.7074 (t0) REVERT: A 732 MET cc_start: 0.6167 (tpt) cc_final: 0.5818 (mmm) REVERT: A 734 PHE cc_start: 0.7716 (t80) cc_final: 0.7406 (t80) REVERT: A 738 GLN cc_start: 0.6367 (mm110) cc_final: 0.6090 (mp10) REVERT: A 745 MET cc_start: 0.7660 (tpt) cc_final: 0.7032 (mmm) REVERT: A 772 MET cc_start: 0.6784 (mtp) cc_final: 0.6573 (mtp) REVERT: A 777 ARG cc_start: 0.6346 (mtm110) cc_final: 0.6063 (mtm-85) REVERT: A 794 PHE cc_start: 0.8273 (p90) cc_final: 0.7851 (p90) REVERT: A 811 MET cc_start: 0.7497 (mtp) cc_final: 0.7234 (mtm) REVERT: A 852 ARG cc_start: 0.6127 (mtm-85) cc_final: 0.5887 (mtm-85) REVERT: A 886 LYS cc_start: 0.7467 (ptpt) cc_final: 0.6555 (pttm) REVERT: A 933 ASP cc_start: 0.7848 (t0) cc_final: 0.6935 (t0) REVERT: B 345 GLU cc_start: 0.6214 (OUTLIER) cc_final: 0.5507 (pm20) REVERT: B 421 ASP cc_start: 0.7912 (t0) cc_final: 0.7444 (m-30) REVERT: B 472 ARG cc_start: 0.5644 (tmm-80) cc_final: 0.5273 (ttm170) REVERT: B 479 MET cc_start: 0.5563 (mtp) cc_final: 0.5198 (mpp) REVERT: B 520 GLU cc_start: 0.7954 (tt0) cc_final: 0.7371 (pm20) REVERT: B 540 ASP cc_start: 0.5896 (t70) cc_final: 0.5475 (t0) REVERT: B 555 GLU cc_start: 0.5824 (tp30) cc_final: 0.5532 (tt0) REVERT: B 559 ILE cc_start: 0.5559 (mt) cc_final: 0.5311 (mp) outliers start: 25 outliers final: 15 residues processed: 178 average time/residue: 1.1996 time to fit residues: 230.6205 Evaluate side-chains 160 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 143 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 529 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 0.0050 chunk 93 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 112 optimal weight: 0.7980 chunk 121 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6218 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10575 Z= 0.175 Angle : 0.520 8.672 14264 Z= 0.271 Chirality : 0.041 0.264 1538 Planarity : 0.004 0.040 1832 Dihedral : 5.856 78.734 1393 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.26 % Allowed : 12.79 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.25), residues: 1241 helix: 1.67 (0.22), residues: 594 sheet: -0.46 (0.43), residues: 155 loop : -0.51 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 552 HIS 0.003 0.001 HIS A 665 PHE 0.022 0.002 PHE A 977 TYR 0.019 0.001 TYR A 182 ARG 0.003 0.000 ARG A 79 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 162 time to evaluate : 1.219 Fit side-chains revert: symmetry clash REVERT: A 75 GLN cc_start: 0.7330 (mm110) cc_final: 0.6999 (mp-120) REVERT: A 76 GLU cc_start: 0.5786 (mt-10) cc_final: 0.5394 (tm-30) REVERT: A 127 GLU cc_start: 0.6274 (mm-30) cc_final: 0.5899 (mt-10) REVERT: A 130 MET cc_start: 0.6685 (mmm) cc_final: 0.5775 (mmt) REVERT: A 152 ASP cc_start: 0.7217 (m-30) cc_final: 0.6859 (m-30) REVERT: A 179 LYS cc_start: 0.6294 (tptp) cc_final: 0.5871 (mttm) REVERT: A 265 TYR cc_start: 0.6428 (m-10) cc_final: 0.6130 (m-10) REVERT: A 282 MET cc_start: 0.6748 (tpp) cc_final: 0.6347 (tpp) REVERT: A 384 ASN cc_start: 0.7935 (t0) cc_final: 0.6755 (m-40) REVERT: A 441 MET cc_start: 0.7680 (ttm) cc_final: 0.7237 (ttm) REVERT: A 453 GLU cc_start: 0.6118 (tt0) cc_final: 0.5570 (tm-30) REVERT: A 549 ASP cc_start: 0.5918 (t0) cc_final: 0.5532 (m-30) REVERT: A 677 ASN cc_start: 0.7781 (t0) cc_final: 0.7205 (t0) REVERT: A 732 MET cc_start: 0.6126 (tpt) cc_final: 0.5722 (mmm) REVERT: A 745 MET cc_start: 0.7671 (tpt) cc_final: 0.7140 (mmm) REVERT: A 767 GLU cc_start: 0.6288 (pm20) cc_final: 0.5589 (pm20) REVERT: A 768 GLU cc_start: 0.7013 (mm-30) cc_final: 0.6600 (mp0) REVERT: A 777 ARG cc_start: 0.6393 (mtm110) cc_final: 0.6143 (mtm-85) REVERT: A 780 TRP cc_start: 0.7882 (t-100) cc_final: 0.7230 (t-100) REVERT: A 789 MET cc_start: 0.6823 (mtt) cc_final: 0.6461 (mtm) REVERT: A 794 PHE cc_start: 0.8208 (p90) cc_final: 0.7811 (p90) REVERT: A 811 MET cc_start: 0.7496 (mtp) cc_final: 0.7268 (mtm) REVERT: A 822 ASN cc_start: 0.6578 (t0) cc_final: 0.5719 (m-40) REVERT: A 852 ARG cc_start: 0.6103 (mtm-85) cc_final: 0.5843 (mtm-85) REVERT: A 886 LYS cc_start: 0.7421 (ptpt) cc_final: 0.6519 (pttm) REVERT: A 933 ASP cc_start: 0.7726 (t0) cc_final: 0.6772 (t0) REVERT: A 975 ARG cc_start: 0.6873 (tmm160) cc_final: 0.6605 (tmm160) REVERT: A 977 PHE cc_start: 0.7101 (t80) cc_final: 0.6851 (t80) REVERT: B 421 ASP cc_start: 0.7827 (t0) cc_final: 0.7444 (m-30) REVERT: B 426 TYR cc_start: 0.7220 (m-80) cc_final: 0.6972 (m-80) REVERT: B 472 ARG cc_start: 0.5726 (tmm-80) cc_final: 0.5430 (ttm170) REVERT: B 479 MET cc_start: 0.5427 (mtp) cc_final: 0.5096 (mpp) REVERT: B 520 GLU cc_start: 0.7830 (tt0) cc_final: 0.7331 (pm20) REVERT: B 540 ASP cc_start: 0.5774 (t70) cc_final: 0.5336 (t0) REVERT: B 555 GLU cc_start: 0.6131 (tp30) cc_final: 0.5803 (tt0) REVERT: B 559 ILE cc_start: 0.5697 (mt) cc_final: 0.5446 (mp) outliers start: 26 outliers final: 14 residues processed: 175 average time/residue: 1.1793 time to fit residues: 223.0002 Evaluate side-chains 163 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 149 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 922 MET Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain B residue 364 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 ASN A 931 HIS ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6261 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 10575 Z= 0.326 Angle : 0.596 8.906 14264 Z= 0.308 Chirality : 0.045 0.277 1538 Planarity : 0.004 0.042 1832 Dihedral : 6.258 85.659 1393 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.66 % Allowed : 13.84 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.24), residues: 1241 helix: 1.41 (0.22), residues: 593 sheet: -0.46 (0.42), residues: 154 loop : -0.72 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 552 HIS 0.005 0.001 HIS A 362 PHE 0.025 0.002 PHE A 667 TYR 0.019 0.002 TYR B 470 ARG 0.005 0.000 ARG A 154 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 154 time to evaluate : 1.351 Fit side-chains revert: symmetry clash REVERT: A 75 GLN cc_start: 0.7337 (mm110) cc_final: 0.7007 (mp-120) REVERT: A 76 GLU cc_start: 0.5958 (mt-10) cc_final: 0.5527 (tm-30) REVERT: A 127 GLU cc_start: 0.6453 (mm-30) cc_final: 0.6006 (mt-10) REVERT: A 130 MET cc_start: 0.6691 (mmm) cc_final: 0.5783 (mmt) REVERT: A 179 LYS cc_start: 0.6258 (tptp) cc_final: 0.5863 (mmmm) REVERT: A 249 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.7192 (tmtt) REVERT: A 265 TYR cc_start: 0.6459 (m-10) cc_final: 0.6170 (m-10) REVERT: A 282 MET cc_start: 0.6717 (tpp) cc_final: 0.6337 (tpp) REVERT: A 352 ASP cc_start: 0.7505 (OUTLIER) cc_final: 0.7086 (m-30) REVERT: A 384 ASN cc_start: 0.7899 (t0) cc_final: 0.6730 (m-40) REVERT: A 441 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.7449 (ttm) REVERT: A 453 GLU cc_start: 0.6029 (tt0) cc_final: 0.5567 (tm-30) REVERT: A 549 ASP cc_start: 0.5961 (t0) cc_final: 0.5520 (m-30) REVERT: A 677 ASN cc_start: 0.7935 (t0) cc_final: 0.7402 (t0) REVERT: A 732 MET cc_start: 0.6169 (tpt) cc_final: 0.5816 (mmm) REVERT: A 739 MET cc_start: 0.8424 (mtt) cc_final: 0.8172 (mtt) REVERT: A 745 MET cc_start: 0.7666 (tpt) cc_final: 0.7134 (mmm) REVERT: A 767 GLU cc_start: 0.6323 (pm20) cc_final: 0.5670 (pm20) REVERT: A 768 GLU cc_start: 0.7045 (mm-30) cc_final: 0.6650 (mp0) REVERT: A 794 PHE cc_start: 0.8201 (p90) cc_final: 0.7769 (p90) REVERT: A 811 MET cc_start: 0.7575 (mtp) cc_final: 0.7337 (mtm) REVERT: A 822 ASN cc_start: 0.6652 (t0) cc_final: 0.5798 (m-40) REVERT: A 852 ARG cc_start: 0.6183 (mtm-85) cc_final: 0.5881 (mtm-85) REVERT: A 886 LYS cc_start: 0.7452 (ptpt) cc_final: 0.6516 (pttm) REVERT: A 933 ASP cc_start: 0.7799 (t0) cc_final: 0.6849 (t0) REVERT: B 421 ASP cc_start: 0.7859 (t0) cc_final: 0.7554 (m-30) REVERT: B 472 ARG cc_start: 0.5547 (tmm-80) cc_final: 0.5305 (ttm170) REVERT: B 479 MET cc_start: 0.5448 (mtp) cc_final: 0.5051 (mpp) REVERT: B 520 GLU cc_start: 0.7813 (tt0) cc_final: 0.7289 (pm20) REVERT: B 540 ASP cc_start: 0.5788 (t70) cc_final: 0.5380 (t0) REVERT: B 547 GLU cc_start: 0.6493 (mm-30) cc_final: 0.6016 (mt-10) REVERT: B 555 GLU cc_start: 0.6292 (tp30) cc_final: 0.5990 (tt0) outliers start: 42 outliers final: 19 residues processed: 177 average time/residue: 1.1108 time to fit residues: 212.9356 Evaluate side-chains 172 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 150 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 993 GLN Chi-restraints excluded: chain B residue 364 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 0 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 879 GLN ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 457 GLN B 527 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6228 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10575 Z= 0.187 Angle : 0.516 8.878 14264 Z= 0.269 Chirality : 0.041 0.272 1538 Planarity : 0.004 0.042 1832 Dihedral : 6.139 88.125 1393 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.22 % Allowed : 15.14 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.24), residues: 1241 helix: 1.60 (0.22), residues: 594 sheet: -0.37 (0.43), residues: 155 loop : -0.61 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 780 HIS 0.003 0.001 HIS A 665 PHE 0.021 0.002 PHE A 667 TYR 0.015 0.001 TYR B 470 ARG 0.002 0.000 ARG A 975 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 157 time to evaluate : 1.078 Fit side-chains revert: symmetry clash REVERT: A 75 GLN cc_start: 0.7269 (mm110) cc_final: 0.6942 (mp-120) REVERT: A 76 GLU cc_start: 0.5954 (mt-10) cc_final: 0.5502 (tm-30) REVERT: A 83 PHE cc_start: 0.7375 (m-80) cc_final: 0.6981 (m-80) REVERT: A 127 GLU cc_start: 0.6500 (mm-30) cc_final: 0.6043 (mt-10) REVERT: A 130 MET cc_start: 0.6697 (mmm) cc_final: 0.5750 (mmt) REVERT: A 179 LYS cc_start: 0.6265 (tptp) cc_final: 0.5860 (mttm) REVERT: A 265 TYR cc_start: 0.6417 (m-10) cc_final: 0.6118 (m-10) REVERT: A 282 MET cc_start: 0.6693 (tpp) cc_final: 0.6367 (tpp) REVERT: A 352 ASP cc_start: 0.7431 (OUTLIER) cc_final: 0.6978 (m-30) REVERT: A 384 ASN cc_start: 0.7891 (t0) cc_final: 0.6695 (m-40) REVERT: A 441 MET cc_start: 0.7773 (ttm) cc_final: 0.7457 (ttm) REVERT: A 453 GLU cc_start: 0.5910 (tt0) cc_final: 0.5457 (tm-30) REVERT: A 677 ASN cc_start: 0.7884 (t0) cc_final: 0.7363 (t0) REVERT: A 732 MET cc_start: 0.6128 (tpt) cc_final: 0.5749 (mmm) REVERT: A 745 MET cc_start: 0.7648 (tpt) cc_final: 0.7162 (mmm) REVERT: A 767 GLU cc_start: 0.6282 (pm20) cc_final: 0.5639 (pm20) REVERT: A 768 GLU cc_start: 0.6924 (mm-30) cc_final: 0.6599 (mp0) REVERT: A 780 TRP cc_start: 0.7877 (t-100) cc_final: 0.7233 (t-100) REVERT: A 789 MET cc_start: 0.6836 (mtt) cc_final: 0.6382 (mtm) REVERT: A 794 PHE cc_start: 0.8217 (p90) cc_final: 0.7809 (p90) REVERT: A 811 MET cc_start: 0.7524 (mtp) cc_final: 0.7258 (mtm) REVERT: A 822 ASN cc_start: 0.6635 (t0) cc_final: 0.5780 (m-40) REVERT: A 852 ARG cc_start: 0.6176 (mtm-85) cc_final: 0.5826 (mtm-85) REVERT: A 886 LYS cc_start: 0.7294 (ptpt) cc_final: 0.6410 (pttm) REVERT: A 933 ASP cc_start: 0.7848 (t0) cc_final: 0.6833 (t0) REVERT: A 956 LEU cc_start: 0.7444 (mt) cc_final: 0.7237 (tp) REVERT: A 977 PHE cc_start: 0.6948 (t80) cc_final: 0.6669 (t80) REVERT: A 1029 ASP cc_start: 0.6957 (m-30) cc_final: 0.6548 (m-30) REVERT: B 364 MET cc_start: 0.5590 (OUTLIER) cc_final: 0.5054 (tmt) REVERT: B 421 ASP cc_start: 0.7902 (t0) cc_final: 0.7639 (m-30) REVERT: B 426 TYR cc_start: 0.7276 (m-80) cc_final: 0.7057 (m-80) REVERT: B 479 MET cc_start: 0.5516 (mtp) cc_final: 0.5120 (mpp) REVERT: B 520 GLU cc_start: 0.7784 (tt0) cc_final: 0.7308 (pm20) REVERT: B 540 ASP cc_start: 0.5770 (t70) cc_final: 0.5423 (t0) REVERT: B 547 GLU cc_start: 0.6372 (mm-30) cc_final: 0.5912 (mt-10) REVERT: B 555 GLU cc_start: 0.6250 (tp30) cc_final: 0.5923 (tt0) outliers start: 37 outliers final: 17 residues processed: 179 average time/residue: 1.1857 time to fit residues: 229.5596 Evaluate side-chains 169 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 150 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 993 GLN Chi-restraints excluded: chain B residue 364 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 70 optimal weight: 0.0670 chunk 29 optimal weight: 0.8980 chunk 119 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 879 GLN B 527 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6242 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10575 Z= 0.236 Angle : 0.541 8.907 14264 Z= 0.280 Chirality : 0.042 0.287 1538 Planarity : 0.004 0.043 1832 Dihedral : 6.213 89.053 1393 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.31 % Allowed : 16.62 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.25), residues: 1241 helix: 1.56 (0.22), residues: 594 sheet: -0.42 (0.43), residues: 159 loop : -0.65 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 552 HIS 0.003 0.001 HIS A 665 PHE 0.023 0.002 PHE A 667 TYR 0.022 0.002 TYR A 182 ARG 0.003 0.000 ARG A 916 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 151 time to evaluate : 1.063 Fit side-chains revert: symmetry clash REVERT: A 75 GLN cc_start: 0.7348 (mm110) cc_final: 0.6995 (mp-120) REVERT: A 76 GLU cc_start: 0.5832 (mt-10) cc_final: 0.5397 (tm-30) REVERT: A 127 GLU cc_start: 0.6550 (mm-30) cc_final: 0.6078 (mt-10) REVERT: A 130 MET cc_start: 0.6627 (mmm) cc_final: 0.5706 (mmt) REVERT: A 179 LYS cc_start: 0.6293 (tptp) cc_final: 0.5869 (mttm) REVERT: A 249 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.7145 (tmtt) REVERT: A 265 TYR cc_start: 0.6364 (m-10) cc_final: 0.6060 (m-10) REVERT: A 282 MET cc_start: 0.6699 (tpp) cc_final: 0.6367 (tpp) REVERT: A 352 ASP cc_start: 0.7440 (OUTLIER) cc_final: 0.7068 (m-30) REVERT: A 384 ASN cc_start: 0.7909 (t0) cc_final: 0.6704 (m-40) REVERT: A 441 MET cc_start: 0.7776 (OUTLIER) cc_final: 0.7459 (ttm) REVERT: A 453 GLU cc_start: 0.6020 (tt0) cc_final: 0.5532 (tm-30) REVERT: A 549 ASP cc_start: 0.5870 (t0) cc_final: 0.5494 (m-30) REVERT: A 677 ASN cc_start: 0.7859 (t0) cc_final: 0.7338 (t0) REVERT: A 732 MET cc_start: 0.6051 (tpt) cc_final: 0.5679 (mmm) REVERT: A 745 MET cc_start: 0.7652 (tpt) cc_final: 0.7158 (mmm) REVERT: A 768 GLU cc_start: 0.6981 (mm-30) cc_final: 0.6706 (mp0) REVERT: A 780 TRP cc_start: 0.7926 (t-100) cc_final: 0.7280 (t-100) REVERT: A 811 MET cc_start: 0.7584 (mtp) cc_final: 0.7310 (mtm) REVERT: A 822 ASN cc_start: 0.6666 (t0) cc_final: 0.5804 (m-40) REVERT: A 886 LYS cc_start: 0.7319 (ptpt) cc_final: 0.6429 (pttm) REVERT: A 933 ASP cc_start: 0.7796 (t0) cc_final: 0.6757 (t0) REVERT: A 977 PHE cc_start: 0.7061 (t80) cc_final: 0.6669 (t80) REVERT: A 1029 ASP cc_start: 0.6959 (m-30) cc_final: 0.6546 (m-30) REVERT: B 364 MET cc_start: 0.5589 (OUTLIER) cc_final: 0.5138 (tmt) REVERT: B 421 ASP cc_start: 0.7894 (t0) cc_final: 0.7584 (m-30) REVERT: B 426 TYR cc_start: 0.7358 (m-80) cc_final: 0.7149 (m-80) REVERT: B 479 MET cc_start: 0.5559 (mtp) cc_final: 0.5156 (mpp) REVERT: B 520 GLU cc_start: 0.7758 (tt0) cc_final: 0.7183 (pm20) REVERT: B 540 ASP cc_start: 0.5784 (t70) cc_final: 0.5397 (t0) REVERT: B 547 GLU cc_start: 0.6412 (mm-30) cc_final: 0.5967 (mt-10) REVERT: B 555 GLU cc_start: 0.6307 (tp30) cc_final: 0.5740 (tt0) REVERT: B 559 ILE cc_start: 0.5664 (mt) cc_final: 0.5362 (mp) outliers start: 38 outliers final: 19 residues processed: 174 average time/residue: 1.1263 time to fit residues: 211.9061 Evaluate side-chains 168 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 145 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 993 GLN Chi-restraints excluded: chain B residue 364 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.1929 > 50: distance: 15 - 35: 18.767 distance: 19 - 44: 17.465 distance: 24 - 55: 22.973 distance: 28 - 35: 16.064 distance: 29 - 67: 23.773 distance: 35 - 36: 29.306 distance: 36 - 37: 45.199 distance: 36 - 39: 11.472 distance: 37 - 38: 45.353 distance: 37 - 44: 49.736 distance: 38 - 73: 42.337 distance: 39 - 40: 6.615 distance: 40 - 41: 3.542 distance: 41 - 42: 3.055 distance: 41 - 43: 6.802 distance: 44 - 45: 54.027 distance: 45 - 46: 61.193 distance: 45 - 48: 35.405 distance: 46 - 47: 28.347 distance: 46 - 55: 38.629 distance: 48 - 49: 9.592 distance: 49 - 50: 4.944 distance: 50 - 51: 5.269 distance: 51 - 52: 6.554 distance: 52 - 53: 4.927 distance: 52 - 54: 6.263 distance: 55 - 56: 44.654 distance: 56 - 57: 50.270 distance: 56 - 59: 40.096 distance: 57 - 58: 23.969 distance: 57 - 67: 44.283 distance: 59 - 60: 41.249 distance: 60 - 61: 19.923 distance: 60 - 62: 18.668 distance: 61 - 63: 9.119 distance: 62 - 64: 13.073 distance: 63 - 65: 10.902 distance: 64 - 65: 11.904 distance: 65 - 66: 8.790 distance: 67 - 68: 37.002 distance: 68 - 69: 15.827 distance: 68 - 71: 11.445 distance: 69 - 70: 13.993 distance: 69 - 73: 44.461 distance: 71 - 72: 38.812 distance: 73 - 74: 41.399 distance: 74 - 75: 44.486 distance: 74 - 77: 50.533 distance: 75 - 76: 15.655 distance: 75 - 82: 33.142 distance: 77 - 78: 27.950 distance: 78 - 79: 21.944 distance: 79 - 80: 4.825 distance: 80 - 81: 11.938 distance: 82 - 83: 29.249 distance: 83 - 84: 55.501 distance: 83 - 86: 23.127 distance: 84 - 85: 47.547 distance: 84 - 91: 43.428 distance: 86 - 87: 39.238 distance: 87 - 88: 11.544 distance: 88 - 89: 24.354 distance: 88 - 90: 13.208 distance: 91 - 92: 16.153 distance: 92 - 93: 19.302 distance: 92 - 95: 4.948 distance: 93 - 94: 30.726 distance: 93 - 103: 7.941 distance: 95 - 96: 6.146 distance: 96 - 97: 6.776 distance: 96 - 98: 8.734 distance: 97 - 99: 7.719 distance: 98 - 100: 7.924 distance: 99 - 101: 15.741 distance: 100 - 101: 10.725 distance: 101 - 102: 10.477 distance: 103 - 104: 4.542 distance: 104 - 105: 27.191 distance: 105 - 106: 25.468 distance: 105 - 111: 11.501 distance: 107 - 108: 5.466 distance: 107 - 109: 11.066 distance: 108 - 110: 15.034 distance: 111 - 112: 15.518 distance: 112 - 113: 25.828 distance: 112 - 115: 7.225 distance: 113 - 114: 6.414 distance: 113 - 120: 23.536 distance: 115 - 116: 7.605 distance: 116 - 117: 15.823 distance: 117 - 118: 4.798 distance: 117 - 119: 13.641 distance: 120 - 121: 7.142 distance: 121 - 122: 8.748 distance: 121 - 124: 15.185 distance: 122 - 123: 21.359 distance: 122 - 129: 12.060 distance: 124 - 125: 24.740 distance: 125 - 126: 29.064 distance: 126 - 127: 23.735 distance: 127 - 128: 4.943