Starting phenix.real_space_refine on Fri Jan 19 04:29:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ilr_35543/01_2024/8ilr_35543_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ilr_35543/01_2024/8ilr_35543.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ilr_35543/01_2024/8ilr_35543.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ilr_35543/01_2024/8ilr_35543.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ilr_35543/01_2024/8ilr_35543_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ilr_35543/01_2024/8ilr_35543_updated.pdb" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.105 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 73 5.16 5 C 6603 2.51 5 N 1792 2.21 5 O 1906 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 495": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 10374 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7981 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 977, 7981 Classifications: {'peptide': 977} Link IDs: {'PTRANS': 47, 'TRANS': 929} Chain breaks: 5 Chain: "B" Number of atoms: 2346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2346 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 4, 'TRANS': 271} Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 47 Unusual residues: {'7TZ': 1} Classifications: {'undetermined': 1, 'water': 7} Link IDs: {None: 7} Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N BGLU A 950 " occ=0.46 ... (7 atoms not shown) pdb=" OE2BGLU A 950 " occ=0.46 residue: pdb=" N BARG A 951 " occ=0.46 ... (9 atoms not shown) pdb=" NH2BARG A 951 " occ=0.46 residue: pdb=" N BPRO A 953 " occ=0.46 ... (5 atoms not shown) pdb=" CD BPRO A 953 " occ=0.46 residue: pdb=" N BVAL A 955 " occ=0.46 ... (5 atoms not shown) pdb=" CG2BVAL A 955 " occ=0.46 residue: pdb=" N BLEU A 956 " occ=0.50 ... (6 atoms not shown) pdb=" CD2BLEU A 956 " occ=0.50 Time building chain proxies: 6.29, per 1000 atoms: 0.61 Number of scatterers: 10374 At special positions: 0 Unit cell: (86.751, 112.455, 129.591, 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 73 16.00 O 1906 8.00 N 1792 7.00 C 6603 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.22 Conformation dependent library (CDL) restraints added in 1.9 seconds 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2398 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 9 sheets defined 45.6% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.86 Creating SS restraints... Processing helix chain 'A' and resid 42 through 52 removed outlier: 3.709A pdb=" N GLU A 52 " --> pdb=" O GLU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 92 Processing helix chain 'A' and resid 110 through 121 Processing helix chain 'A' and resid 125 through 130 Processing helix chain 'A' and resid 134 through 154 removed outlier: 3.970A pdb=" N LEU A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ASN A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N VAL A 146 " --> pdb=" O ASN A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 166 Processing helix chain 'A' and resid 179 through 184 Processing helix chain 'A' and resid 200 through 202 No H-bonds generated for 'chain 'A' and resid 200 through 202' Processing helix chain 'A' and resid 217 through 227 removed outlier: 3.811A pdb=" N LYS A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 269 No H-bonds generated for 'chain 'A' and resid 267 through 269' Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 290 through 296 removed outlier: 3.820A pdb=" N GLN A 296 " --> pdb=" O SER A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 309 Processing helix chain 'A' and resid 327 through 329 No H-bonds generated for 'chain 'A' and resid 327 through 329' Processing helix chain 'A' and resid 393 through 395 No H-bonds generated for 'chain 'A' and resid 393 through 395' Processing helix chain 'A' and resid 489 through 495 Processing helix chain 'A' and resid 529 through 536 Processing helix chain 'A' and resid 545 through 553 removed outlier: 3.805A pdb=" N SER A 553 " --> pdb=" O ASP A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 558 No H-bonds generated for 'chain 'A' and resid 556 through 558' Processing helix chain 'A' and resid 562 through 568 Proline residue: A 566 - end of helix Processing helix chain 'A' and resid 577 through 588 removed outlier: 3.520A pdb=" N GLN A 582 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N CYS A 585 " --> pdb=" O ALA A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 598 No H-bonds generated for 'chain 'A' and resid 595 through 598' Processing helix chain 'A' and resid 600 through 602 No H-bonds generated for 'chain 'A' and resid 600 through 602' Processing helix chain 'A' and resid 609 through 622 removed outlier: 3.595A pdb=" N LYS A 621 " --> pdb=" O ARG A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 640 removed outlier: 3.775A pdb=" N GLN A 630 " --> pdb=" O ASP A 626 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ILE A 633 " --> pdb=" O SER A 629 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N GLN A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN A 637 " --> pdb=" O ILE A 633 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LYS A 640 " --> pdb=" O VAL A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 657 Processing helix chain 'A' and resid 661 through 674 removed outlier: 3.642A pdb=" N GLU A 674 " --> pdb=" O HIS A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 694 Processing helix chain 'A' and resid 697 through 719 removed outlier: 3.583A pdb=" N LEU A 702 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN A 705 " --> pdb=" O LEU A 702 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL A 706 " --> pdb=" O ASN A 703 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU A 707 " --> pdb=" O ARG A 704 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 712 " --> pdb=" O MET A 709 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU A 719 " --> pdb=" O THR A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 739 removed outlier: 3.759A pdb=" N MET A 739 " --> pdb=" O LEU A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 747 removed outlier: 3.517A pdb=" N ALA A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 768 No H-bonds generated for 'chain 'A' and resid 766 through 768' Processing helix chain 'A' and resid 808 through 827 removed outlier: 3.562A pdb=" N GLN A 815 " --> pdb=" O MET A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 863 Processing helix chain 'A' and resid 876 through 884 Processing helix chain 'A' and resid 889 through 911 Processing helix chain 'A' and resid 958 through 964 removed outlier: 3.800A pdb=" N ILE A 962 " --> pdb=" O GLN A 958 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL A 963 " --> pdb=" O ASP A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 1004 removed outlier: 3.621A pdb=" N HIS A 994 " --> pdb=" O ALA A 990 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ASN A 996 " --> pdb=" O ARG A 992 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU A 997 " --> pdb=" O GLN A 993 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE A 998 " --> pdb=" O HIS A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1008 No H-bonds generated for 'chain 'A' and resid 1006 through 1008' Processing helix chain 'A' and resid 1016 through 1025 removed outlier: 4.375A pdb=" N TYR A1021 " --> pdb=" O ASP A1017 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ILE A1022 " --> pdb=" O ASP A1018 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG A1023 " --> pdb=" O ILE A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1047 removed outlier: 3.703A pdb=" N GLU A1037 " --> pdb=" O GLN A1033 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 330 No H-bonds generated for 'chain 'B' and resid 328 through 330' Processing helix chain 'B' and resid 340 through 347 removed outlier: 3.511A pdb=" N GLU B 345 " --> pdb=" O GLU B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 409 Processing helix chain 'B' and resid 413 through 415 No H-bonds generated for 'chain 'B' and resid 413 through 415' Processing helix chain 'B' and resid 432 through 434 No H-bonds generated for 'chain 'B' and resid 432 through 434' Processing helix chain 'B' and resid 442 through 504 removed outlier: 3.577A pdb=" N GLU B 489 " --> pdb=" O GLU B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 514 Processing helix chain 'B' and resid 518 through 586 Proline residue: B 568 - end of helix Processing helix chain 'B' and resid 591 through 597 Processing sheet with id= A, first strand: chain 'A' and resid 31 through 37 removed outlier: 3.855A pdb=" N VAL A 32 " --> pdb=" O CYS A 24 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N CYS A 36 " --> pdb=" O ILE A 20 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ILE A 20 " --> pdb=" O CYS A 36 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 208 through 212 Processing sheet with id= C, first strand: chain 'A' and resid 324 through 326 removed outlier: 6.277A pdb=" N VAL A 483 " --> pdb=" O LYS A 325 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 385 through 388 removed outlier: 3.778A pdb=" N GLU A 385 " --> pdb=" O ILE A 338 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 353 through 362 removed outlier: 3.720A pdb=" N LYS A 353 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA A 423 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N SER A 408 " --> pdb=" O PRO A 421 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 779 through 782 Processing sheet with id= G, first strand: chain 'A' and resid 854 through 856 Processing sheet with id= H, first strand: chain 'B' and resid 355 through 358 Processing sheet with id= I, first strand: chain 'B' and resid 384 through 386 413 hydrogen bonds defined for protein. 1158 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: 3.53 Time building geometry restraints manager: 4.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1825 1.32 - 1.44: 2672 1.44 - 1.57: 5975 1.57 - 1.69: 2 1.69 - 1.81: 114 Bond restraints: 10588 Sorted by residual: bond pdb=" CA ARG A 777 " pdb=" C ARG A 777 " ideal model delta sigma weight residual 1.524 1.479 0.045 1.26e-02 6.30e+03 1.25e+01 bond pdb=" C16 7TZ A1101 " pdb=" N18 7TZ A1101 " ideal model delta sigma weight residual 1.301 1.359 -0.058 2.00e-02 2.50e+03 8.30e+00 bond pdb=" C ARG A 777 " pdb=" O ARG A 777 " ideal model delta sigma weight residual 1.238 1.201 0.037 1.28e-02 6.10e+03 8.21e+00 bond pdb=" C14 7TZ A1101 " pdb=" N13 7TZ A1101 " ideal model delta sigma weight residual 1.302 1.356 -0.054 2.00e-02 2.50e+03 7.24e+00 bond pdb=" C39 7TZ A1101 " pdb=" N40 7TZ A1101 " ideal model delta sigma weight residual 1.302 1.355 -0.053 2.00e-02 2.50e+03 7.12e+00 ... (remaining 10583 not shown) Histogram of bond angle deviations from ideal: 100.38 - 114.73: 6633 114.73 - 129.08: 7571 129.08 - 143.43: 76 143.43 - 157.78: 0 157.78 - 172.14: 2 Bond angle restraints: 14282 Sorted by residual: angle pdb=" C ARG A 777 " pdb=" N PRO A 778 " pdb=" CA PRO A 778 " ideal model delta sigma weight residual 119.85 111.66 8.19 1.01e+00 9.80e-01 6.57e+01 angle pdb=" N ASN B 325 " pdb=" CA ASN B 325 " pdb=" C ASN B 325 " ideal model delta sigma weight residual 107.37 117.92 -10.55 2.07e+00 2.33e-01 2.60e+01 angle pdb=" CA PRO A 97 " pdb=" N PRO A 97 " pdb=" CD PRO A 97 " ideal model delta sigma weight residual 112.00 106.97 5.03 1.40e+00 5.10e-01 1.29e+01 angle pdb=" N ALA A 775 " pdb=" CA ALA A 775 " pdb=" C ALA A 775 " ideal model delta sigma weight residual 110.80 118.00 -7.20 2.13e+00 2.20e-01 1.14e+01 angle pdb=" C ASN B 325 " pdb=" CA ASN B 325 " pdb=" CB ASN B 325 " ideal model delta sigma weight residual 111.82 107.55 4.27 1.38e+00 5.25e-01 9.56e+00 ... (remaining 14277 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 5560 17.73 - 35.47: 724 35.47 - 53.20: 152 53.20 - 70.94: 23 70.94 - 88.67: 10 Dihedral angle restraints: 6469 sinusoidal: 2774 harmonic: 3695 Sorted by residual: dihedral pdb=" C ARG A 777 " pdb=" N ARG A 777 " pdb=" CA ARG A 777 " pdb=" CB ARG A 777 " ideal model delta harmonic sigma weight residual -122.60 -134.69 12.09 0 2.50e+00 1.60e-01 2.34e+01 dihedral pdb=" N ARG A 777 " pdb=" C ARG A 777 " pdb=" CA ARG A 777 " pdb=" CB ARG A 777 " ideal model delta harmonic sigma weight residual 122.80 134.42 -11.62 0 2.50e+00 1.60e-01 2.16e+01 dihedral pdb=" CB GLU A 768 " pdb=" CG GLU A 768 " pdb=" CD GLU A 768 " pdb=" OE1 GLU A 768 " ideal model delta sinusoidal sigma weight residual 0.00 88.67 -88.67 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 6466 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 1532 0.118 - 0.237: 5 0.237 - 0.355: 0 0.355 - 0.474: 0 0.474 - 0.592: 1 Chirality restraints: 1538 Sorted by residual: chirality pdb=" CA ARG A 777 " pdb=" N ARG A 777 " pdb=" C ARG A 777 " pdb=" CB ARG A 777 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.76e+00 chirality pdb=" CA ALA A 775 " pdb=" N ALA A 775 " pdb=" C ALA A 775 " pdb=" CB ALA A 775 " both_signs ideal model delta sigma weight residual False 2.48 2.28 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA ASN B 325 " pdb=" N ASN B 325 " pdb=" C ASN B 325 " pdb=" CB ASN B 325 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 3.98e-01 ... (remaining 1535 not shown) Planarity restraints: 1835 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C22 7TZ A1101 " 0.153 2.00e-02 2.50e+03 8.10e-02 1.48e+02 pdb=" C23 7TZ A1101 " 0.008 2.00e-02 2.50e+03 pdb=" C24 7TZ A1101 " -0.055 2.00e-02 2.50e+03 pdb=" C25 7TZ A1101 " -0.056 2.00e-02 2.50e+03 pdb=" C26 7TZ A1101 " -0.051 2.00e-02 2.50e+03 pdb=" C27 7TZ A1101 " -0.095 2.00e-02 2.50e+03 pdb=" C28 7TZ A1101 " -0.053 2.00e-02 2.50e+03 pdb=" C29 7TZ A1101 " 0.030 2.00e-02 2.50e+03 pdb=" C30 7TZ A1101 " 0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C29 7TZ A1101 " -0.149 2.00e-02 2.50e+03 6.54e-02 1.28e+02 pdb=" C30 7TZ A1101 " 0.001 2.00e-02 2.50e+03 pdb=" C31 7TZ A1101 " 0.066 2.00e-02 2.50e+03 pdb=" C32 7TZ A1101 " 0.044 2.00e-02 2.50e+03 pdb=" C33 7TZ A1101 " 0.022 2.00e-02 2.50e+03 pdb=" C34 7TZ A1101 " 0.093 2.00e-02 2.50e+03 pdb=" C35 7TZ A1101 " 0.051 2.00e-02 2.50e+03 pdb=" C36 7TZ A1101 " 0.012 2.00e-02 2.50e+03 pdb=" C38 7TZ A1101 " -0.077 2.00e-02 2.50e+03 pdb=" C39 7TZ A1101 " -0.044 2.00e-02 2.50e+03 pdb=" N37 7TZ A1101 " -0.047 2.00e-02 2.50e+03 pdb=" N40 7TZ A1101 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C08 7TZ A1101 " 0.000 2.00e-02 2.50e+03 4.09e-02 5.43e+01 pdb=" C09 7TZ A1101 " 0.036 2.00e-02 2.50e+03 pdb=" C10 7TZ A1101 " 0.055 2.00e-02 2.50e+03 pdb=" C11 7TZ A1101 " -0.007 2.00e-02 2.50e+03 pdb=" C12 7TZ A1101 " -0.047 2.00e-02 2.50e+03 pdb=" C14 7TZ A1101 " -0.020 2.00e-02 2.50e+03 pdb=" C15 7TZ A1101 " 0.084 2.00e-02 2.50e+03 pdb=" C16 7TZ A1101 " -0.015 2.00e-02 2.50e+03 pdb=" C17 7TZ A1101 " 0.033 2.00e-02 2.50e+03 pdb=" C19 7TZ A1101 " -0.027 2.00e-02 2.50e+03 pdb=" C20 7TZ A1101 " 0.007 2.00e-02 2.50e+03 pdb=" N13 7TZ A1101 " -0.069 2.00e-02 2.50e+03 pdb=" N18 7TZ A1101 " -0.031 2.00e-02 2.50e+03 ... (remaining 1832 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 93 2.55 - 3.14: 8530 3.14 - 3.73: 15714 3.73 - 4.31: 22591 4.31 - 4.90: 37731 Nonbonded interactions: 84659 Sorted by model distance: nonbonded pdb=" OD2 ASP A 431 " pdb=" OG1 THR A 433 " model vdw 1.967 2.440 nonbonded pdb=" O GLU A 970 " pdb=" OG1 THR A 974 " model vdw 1.984 2.440 nonbonded pdb=" OG SER B 399 " pdb=" OE1 GLU B 403 " model vdw 2.116 2.440 nonbonded pdb=" OD1 ASN A 428 " pdb=" NE2 GLN A 643 " model vdw 2.130 2.520 nonbonded pdb=" OE1 GLU A 642 " pdb=" O HOH A1201 " model vdw 2.134 2.440 ... (remaining 84654 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.46 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.180 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 32.980 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 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 : 0.003 0.076 10588 Z= 0.164 Angle : 0.447 12.469 14282 Z= 0.231 Chirality : 0.039 0.592 1538 Planarity : 0.005 0.133 1835 Dihedral : 15.946 88.671 4071 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 27.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.46 % Favored : 95.45 % Rotamer: Outliers : 0.35 % Allowed : 15.20 % Favored : 84.45 % Cbeta Deviations : 0.08 % 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: 0.10 (0.25), residues: 1239 helix: 1.22 (0.24), residues: 547 sheet: -1.07 (0.42), residues: 159 loop : -0.73 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 780 HIS 0.002 0.000 HIS A 665 PHE 0.006 0.001 PHE A1039 TYR 0.006 0.001 TYR A 68 ARG 0.003 0.000 ARG B 503 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 143 time to evaluate : 1.226 Fit side-chains revert: symmetry clash REVERT: A 93 ARG cc_start: 0.8181 (mtm-85) cc_final: 0.7797 (mtm-85) REVERT: B 503 ARG cc_start: 0.6996 (tmm160) cc_final: 0.6700 (tmm160) outliers start: 4 outliers final: 1 residues processed: 146 average time/residue: 0.2358 time to fit residues: 48.7836 Evaluate side-chains 142 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 141 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.4980 chunk 93 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 37 optimal weight: 0.0970 chunk 59 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 112 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 630 GLN ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10588 Z= 0.207 Angle : 0.548 6.719 14282 Z= 0.282 Chirality : 0.042 0.182 1538 Planarity : 0.004 0.080 1835 Dihedral : 3.960 34.447 1390 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.87 % Favored : 95.05 % Rotamer: Outliers : 2.00 % Allowed : 14.51 % Favored : 83.49 % 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: 0.00 (0.24), residues: 1239 helix: 1.15 (0.22), residues: 569 sheet: -0.99 (0.41), residues: 143 loop : -0.95 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 780 HIS 0.004 0.001 HIS A 47 PHE 0.014 0.002 PHE A 667 TYR 0.010 0.001 TYR B 334 ARG 0.004 0.000 ARG B 386 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 151 time to evaluate : 1.330 Fit side-chains REVERT: A 93 ARG cc_start: 0.8182 (mtm-85) cc_final: 0.7810 (mtm-85) REVERT: A 148 LYS cc_start: 0.7984 (tppt) cc_final: 0.7516 (ttpp) REVERT: A 179 LYS cc_start: 0.7876 (tppt) cc_final: 0.7613 (mtmt) REVERT: A 599 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.8047 (mtt) REVERT: A 732 MET cc_start: 0.7024 (tpt) cc_final: 0.6709 (mmm) REVERT: A 734 PHE cc_start: 0.8132 (t80) cc_final: 0.7912 (t80) REVERT: A 798 GLU cc_start: 0.7484 (mt-10) cc_final: 0.7241 (mt-10) REVERT: A 1033 GLN cc_start: 0.7655 (tp-100) cc_final: 0.7004 (tt0) REVERT: B 479 MET cc_start: 0.7020 (mtt) cc_final: 0.6774 (mtt) outliers start: 23 outliers final: 10 residues processed: 163 average time/residue: 0.2266 time to fit residues: 53.1583 Evaluate side-chains 151 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 140 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 599 MET Chi-restraints excluded: chain A residue 730 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 810 ASP Chi-restraints excluded: chain B residue 343 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 3.9990 chunk 34 optimal weight: 0.0970 chunk 93 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 112 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 825 GLN B 406 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10588 Z= 0.243 Angle : 0.536 7.558 14282 Z= 0.274 Chirality : 0.041 0.157 1538 Planarity : 0.004 0.061 1835 Dihedral : 3.878 32.103 1388 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.61 % Allowed : 15.90 % Favored : 81.49 % 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: -0.01 (0.24), residues: 1239 helix: 1.26 (0.22), residues: 566 sheet: -1.20 (0.40), residues: 143 loop : -1.03 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 386 HIS 0.006 0.001 HIS A 665 PHE 0.018 0.002 PHE A1039 TYR 0.013 0.001 TYR A 904 ARG 0.005 0.000 ARG A 740 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 151 time to evaluate : 1.339 Fit side-chains REVERT: A 78 GLU cc_start: 0.7339 (tp30) cc_final: 0.6903 (tp30) REVERT: A 148 LYS cc_start: 0.8022 (tppt) cc_final: 0.7517 (ttpp) REVERT: A 732 MET cc_start: 0.7045 (tpt) cc_final: 0.6750 (mmm) REVERT: A 800 ILE cc_start: 0.9007 (OUTLIER) cc_final: 0.8801 (mt) REVERT: B 417 ASN cc_start: 0.6925 (t0) cc_final: 0.6552 (t0) REVERT: B 479 MET cc_start: 0.6947 (mtt) cc_final: 0.6675 (mtt) REVERT: B 582 MET cc_start: 0.7276 (ptt) cc_final: 0.7067 (mtm) outliers start: 30 outliers final: 17 residues processed: 171 average time/residue: 0.2277 time to fit residues: 55.6955 Evaluate side-chains 163 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 145 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 730 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain A residue 810 ASP Chi-restraints excluded: chain A residue 854 SER Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain B residue 356 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 12 optimal weight: 0.3980 chunk 53 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 59 optimal weight: 0.0970 chunk 107 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN A 634 GLN A 815 GLN B 406 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10588 Z= 0.211 Angle : 0.515 7.600 14282 Z= 0.262 Chirality : 0.041 0.149 1538 Planarity : 0.004 0.061 1835 Dihedral : 3.847 31.393 1388 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.78 % Allowed : 16.42 % Favored : 80.80 % 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: 0.07 (0.24), residues: 1239 helix: 1.37 (0.22), residues: 565 sheet: -1.18 (0.39), residues: 145 loop : -1.02 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 669 HIS 0.005 0.001 HIS A 665 PHE 0.014 0.001 PHE A 667 TYR 0.010 0.001 TYR A 904 ARG 0.004 0.000 ARG A 740 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 157 time to evaluate : 1.201 Fit side-chains revert: symmetry clash REVERT: A 79 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7970 (ptm160) REVERT: A 148 LYS cc_start: 0.8045 (tppt) cc_final: 0.7550 (ttpp) REVERT: A 179 LYS cc_start: 0.7803 (tppt) cc_final: 0.7582 (mttt) REVERT: A 732 MET cc_start: 0.7061 (tpt) cc_final: 0.6749 (mmm) REVERT: A 800 ILE cc_start: 0.9026 (OUTLIER) cc_final: 0.8794 (mt) REVERT: A 954 PHE cc_start: 0.5144 (OUTLIER) cc_final: 0.4850 (m-80) REVERT: B 582 MET cc_start: 0.7402 (ptt) cc_final: 0.7138 (mtm) outliers start: 32 outliers final: 20 residues processed: 175 average time/residue: 0.2160 time to fit residues: 54.9336 Evaluate side-chains 167 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 144 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 730 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain A residue 810 ASP Chi-restraints excluded: chain A residue 925 ASP Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 954 PHE Chi-restraints excluded: chain A residue 1017 ASP Chi-restraints excluded: chain A residue 1018 ASP Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 436 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 89 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 chunk 102 optimal weight: 0.4980 chunk 82 optimal weight: 0.0670 chunk 0 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10588 Z= 0.202 Angle : 0.508 8.067 14282 Z= 0.257 Chirality : 0.040 0.144 1538 Planarity : 0.004 0.061 1835 Dihedral : 3.804 30.827 1388 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.04 % Allowed : 17.12 % Favored : 79.84 % 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: 0.17 (0.24), residues: 1239 helix: 1.44 (0.22), residues: 566 sheet: -1.28 (0.37), residues: 161 loop : -0.89 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 669 HIS 0.005 0.001 HIS A 665 PHE 0.014 0.001 PHE A 667 TYR 0.011 0.001 TYR A 904 ARG 0.004 0.000 ARG B 503 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 149 time to evaluate : 1.342 Fit side-chains revert: symmetry clash REVERT: A 148 LYS cc_start: 0.8028 (tppt) cc_final: 0.7548 (ttpp) REVERT: A 179 LYS cc_start: 0.7804 (tppt) cc_final: 0.7587 (mttt) REVERT: A 675 MET cc_start: 0.8483 (mtp) cc_final: 0.8203 (mtp) REVERT: A 732 MET cc_start: 0.7065 (tpt) cc_final: 0.6750 (mmm) REVERT: A 745 MET cc_start: 0.7872 (mmt) cc_final: 0.7440 (mmm) REVERT: A 800 ILE cc_start: 0.9015 (OUTLIER) cc_final: 0.8780 (mt) REVERT: B 582 MET cc_start: 0.7465 (ptt) cc_final: 0.6773 (mmt) outliers start: 35 outliers final: 27 residues processed: 171 average time/residue: 0.2182 time to fit residues: 54.3443 Evaluate side-chains 167 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 139 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 730 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 787 ASP Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain A residue 810 ASP Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 854 SER Chi-restraints excluded: chain A residue 925 ASP Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 1017 ASP Chi-restraints excluded: chain A residue 1018 ASP Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 343 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 99 optimal weight: 0.3980 chunk 55 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 796 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10588 Z= 0.226 Angle : 0.515 8.383 14282 Z= 0.260 Chirality : 0.041 0.146 1538 Planarity : 0.004 0.061 1835 Dihedral : 3.811 29.609 1388 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.95 % Allowed : 17.20 % Favored : 79.84 % 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: 0.17 (0.24), residues: 1239 helix: 1.43 (0.22), residues: 565 sheet: -1.12 (0.39), residues: 144 loop : -0.94 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 669 HIS 0.006 0.001 HIS A 665 PHE 0.014 0.002 PHE A 667 TYR 0.011 0.001 TYR A 904 ARG 0.006 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 146 time to evaluate : 1.324 Fit side-chains revert: symmetry clash REVERT: A 30 MET cc_start: 0.7411 (mpp) cc_final: 0.6851 (mmp) REVERT: A 148 LYS cc_start: 0.8049 (tppt) cc_final: 0.7556 (ttpp) REVERT: A 339 LEU cc_start: 0.8330 (mt) cc_final: 0.8048 (mt) REVERT: A 345 ASN cc_start: 0.7989 (m-40) cc_final: 0.7755 (m-40) REVERT: A 675 MET cc_start: 0.8496 (mtp) cc_final: 0.8182 (mtp) REVERT: A 745 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.7433 (mmm) REVERT: A 800 ILE cc_start: 0.9037 (OUTLIER) cc_final: 0.8807 (mt) REVERT: B 525 MET cc_start: 0.7289 (mmm) cc_final: 0.7047 (mmm) REVERT: B 560 ASP cc_start: 0.7555 (t0) cc_final: 0.7187 (t0) REVERT: B 582 MET cc_start: 0.7472 (ptt) cc_final: 0.6780 (mmt) outliers start: 34 outliers final: 25 residues processed: 167 average time/residue: 0.2004 time to fit residues: 49.9130 Evaluate side-chains 168 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 141 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 730 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 787 ASP Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain A residue 810 ASP Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 925 ASP Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 1017 ASP Chi-restraints excluded: chain A residue 1018 ASP Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 343 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.2026 > 50: distance: 117 - 121: 3.764 distance: 121 - 122: 15.009 distance: 122 - 123: 22.296 distance: 122 - 125: 14.967 distance: 123 - 124: 12.017 distance: 123 - 132: 30.960 distance: 125 - 126: 11.890 distance: 126 - 127: 16.422 distance: 127 - 128: 11.518 distance: 129 - 130: 4.676 distance: 129 - 131: 23.157 distance: 132 - 133: 12.365 distance: 132 - 138: 16.079 distance: 133 - 134: 20.280 distance: 133 - 136: 25.761 distance: 134 - 135: 9.779 distance: 134 - 139: 23.380 distance: 136 - 137: 7.715 distance: 137 - 138: 11.745 distance: 139 - 140: 9.921 distance: 139 - 285: 17.268 distance: 140 - 141: 20.244 distance: 140 - 143: 17.375 distance: 141 - 142: 20.804 distance: 141 - 147: 11.875 distance: 142 - 282: 26.270 distance: 143 - 144: 23.882 distance: 144 - 145: 14.872 distance: 144 - 146: 10.156 distance: 147 - 148: 8.046 distance: 148 - 149: 11.329 distance: 148 - 151: 14.275 distance: 149 - 161: 27.900 distance: 151 - 152: 14.349 distance: 152 - 153: 8.110 distance: 152 - 154: 3.850 distance: 153 - 155: 8.973 distance: 154 - 156: 4.600 distance: 154 - 157: 3.808 distance: 156 - 158: 7.143 distance: 157 - 159: 4.779 distance: 158 - 160: 4.612 distance: 159 - 160: 3.337 distance: 161 - 162: 13.875 distance: 161 - 270: 20.589 distance: 162 - 163: 13.671 distance: 162 - 165: 10.137 distance: 163 - 164: 16.071 distance: 163 - 169: 4.088 distance: 164 - 267: 22.521 distance: 165 - 166: 15.077 distance: 166 - 167: 5.997 distance: 166 - 168: 9.617 distance: 169 - 170: 9.821 distance: 170 - 171: 6.287 distance: 170 - 173: 4.299 distance: 171 - 172: 17.956 distance: 171 - 177: 11.368 distance: 173 - 174: 3.359 distance: 174 - 175: 17.159 distance: 174 - 176: 14.424 distance: 177 - 178: 5.039 distance: 178 - 179: 8.642 distance: 178 - 181: 8.783 distance: 179 - 180: 11.598 distance: 179 - 191: 11.792 distance: 181 - 182: 5.893 distance: 182 - 183: 9.877 distance: 182 - 184: 6.776 distance: 183 - 185: 6.844 distance: 184 - 186: 14.467 distance: 184 - 187: 5.006 distance: 185 - 186: 9.617 distance: 186 - 188: 9.634 distance: 188 - 190: 9.417 distance: 189 - 190: 4.564 distance: 191 - 192: 7.221 distance: 192 - 193: 12.340 distance: 192 - 195: 8.672 distance: 193 - 200: 7.819 distance: 195 - 196: 18.561 distance: 196 - 197: 8.829 distance: 197 - 198: 9.055 distance: 197 - 199: 20.799 distance: 200 - 201: 11.809 distance: 201 - 202: 13.869 distance: 201 - 204: 13.202 distance: 202 - 203: 19.612 distance: 202 - 208: 3.884 distance: 204 - 205: 15.710 distance: 205 - 206: 7.607 distance: 205 - 207: 6.757 distance: 208 - 209: 6.944 distance: 208 - 214: 7.156 distance: 209 - 210: 7.302 distance: 209 - 212: 10.034 distance: 210 - 211: 25.242 distance: 210 - 215: 7.663 distance: 212 - 213: 9.263 distance: 213 - 214: 6.276