Starting phenix.real_space_refine (version: dev) on Sun Feb 19 16:58:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gub_34272/02_2023/8gub_34272_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gub_34272/02_2023/8gub_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_34272/02_2023/8gub_34272.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gub_34272/02_2023/8gub_34272.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gub_34272/02_2023/8gub_34272_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gub_34272/02_2023/8gub_34272_trim_updated.pdb" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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 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-4877/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: 6.00, per 1000 atoms: 0.58 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: 4.03 Conformation dependent library (CDL) restraints added in 1.5 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... running ksdssp... Secondary structure from input PDB file: 45 helices and 8 sheets defined 46.2% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 42 through 55 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) removed outlier: 4.706A pdb=" N LYS A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 92 No H-bonds generated for 'chain 'A' and resid 89 through 92' Processing helix chain 'A' and resid 108 through 121 Processing helix chain 'A' and resid 125 through 130 Processing helix chain 'A' and resid 134 through 154 removed outlier: 4.232A pdb=" N LEU A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ASN A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL A 146 " --> pdb=" O ASN A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 166 Processing helix chain 'A' and resid 179 through 184 removed outlier: 3.569A pdb=" N ASN A 183 " --> pdb=" O LYS A 179 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LYS A 184 " --> pdb=" O HIS A 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 179 through 184' Processing helix chain 'A' and resid 217 through 228 removed outlier: 3.944A pdb=" N ARG A 226 " --> pdb=" O ALA A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 279 Processing helix chain 'A' and resid 290 through 294 Processing helix chain 'A' and resid 306 through 309 No H-bonds generated for '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 498 Processing helix chain 'A' and resid 528 through 535 Processing helix chain 'A' and resid 545 through 557 removed outlier: 5.314A pdb=" N HIS A 556 " --> pdb=" O TRP A 552 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N TYR A 557 " --> pdb=" O SER A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 570 Proline residue: A 562 - end of helix Proline residue: A 566 - end of helix removed outlier: 3.726A pdb=" N LEU A 569 " --> pdb=" O PRO A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 589 removed outlier: 3.604A pdb=" N GLN A 582 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ASP A 589 " --> pdb=" O CYS A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 602 removed outlier: 3.925A pdb=" N GLU A 600 " --> pdb=" O GLU A 596 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU A 601 " --> pdb=" O GLN A 597 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU A 602 " --> pdb=" O ALA A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 622 Processing helix chain 'A' and resid 625 through 630 Processing helix chain 'A' and resid 632 through 640 removed outlier: 3.857A pdb=" N LEU A 639 " --> pdb=" O LEU A 635 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS A 640 " --> pdb=" O VAL A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 657 Processing helix chain 'A' and resid 661 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 681 through 694 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 721 removed outlier: 3.542A pdb=" N LYS A 700 " --> pdb=" O MET A 697 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN A 703 " --> pdb=" O LYS A 700 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU A 707 " --> pdb=" O ARG A 704 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU A 710 " --> pdb=" O GLU A 707 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN A 714 " --> pdb=" O LYS A 711 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLN A 721 " --> pdb=" O ILE A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 740 Processing helix chain 'A' and resid 742 through 747 removed outlier: 3.592A pdb=" N ALA A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 827 Processing helix chain 'A' and resid 857 through 863 Processing helix chain 'A' and resid 876 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 910 removed outlier: 3.562A pdb=" N ARG A 899 " --> pdb=" O LEU A 896 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER A 900 " --> pdb=" O PHE A 897 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA A 902 " --> pdb=" O ARG A 899 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL A 906 " --> pdb=" O GLY A 903 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR A 908 " --> pdb=" O CYS A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 944 Processing helix chain 'A' and resid 958 through 964 Processing helix chain 'A' and resid 975 through 1008 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) removed outlier: 5.253A pdb=" N ASN A 996 " --> pdb=" O ARG A 992 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU A 997 " --> pdb=" O GLN A 993 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE A 998 " --> pdb=" O HIS A 994 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET A1005 " --> pdb=" O LEU A1001 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A1006 " --> pdb=" O PHE A1002 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N GLY A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N SER A1008 " --> pdb=" O MET A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1025 removed outlier: 4.060A pdb=" N TYR A1021 " --> pdb=" O ASP A1017 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE A1022 " --> pdb=" O ASP A1018 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG A1023 " --> pdb=" O ILE A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1049 Processing helix chain 'B' and resid 340 through 346 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 386 through 388 No H-bonds generated for 'chain 'B' and resid 386 through 388' 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 430 through 436 removed outlier: 4.442A pdb=" N VAL B 436 " --> pdb=" O GLN B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 505 Processing helix chain 'B' and resid 519 through 583 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 592 through 595 removed outlier: 3.853A pdb=" N ASN B 595 " --> pdb=" O LYS B 592 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 592 through 595' Processing sheet with id= A, 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: 7.356A pdb=" N PHE A 98 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N VAL A 73 " --> pdb=" O PHE A 98 " (cutoff:3.500A) 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= B, first strand: chain 'A' and resid 205 through 212 removed outlier: 7.520A pdb=" N TRP A 195 " --> pdb=" O PRO A 283 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU A 285 " --> pdb=" O TRP A 195 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 324 through 326 removed outlier: 6.221A 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: 6.890A pdb=" N GLU A 474 " --> pdb=" O LEU A 339 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ALA A 341 " --> pdb=" O CYS A 472 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N CYS A 472 " --> pdb=" O ALA A 341 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 353 through 359 removed outlier: 3.608A pdb=" N LYS A 353 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA A 423 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 6.119A 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 784 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 358 421 hydrogen bonds defined for protein. 1128 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: 3.23 Time building geometry restraints manager: 4.34 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: 5763 17.67 - 35.34: 582 35.34 - 53.01: 92 53.01 - 70.67: 12 70.67 - 88.34: 13 Dihedral angle restraints: 6462 sinusoidal: 2763 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 6459 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: 128 2.58 - 3.16: 9727 3.16 - 3.74: 15723 3.74 - 4.32: 23318 4.32 - 4.90: 37753 Nonbonded interactions: 86649 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 86644 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 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. 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.770 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: 4.290 Check model and map are aligned: 0.160 Process input model: 29.090 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.100 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:12.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6535 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= 0.531 Angle : 0.620 18.425 14264 Z= 0.304 Chirality : 0.041 0.139 1538 Planarity : 0.003 0.037 1832 Dihedral : 14.237 88.342 4062 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 34.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer Outliers : 0.17 % 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 *********************** 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 : 1.317 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 200 average time/residue: 1.2485 time to fit residues: 268.7093 Evaluate side-chains 149 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 148 time to evaluate : 1.231 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.7667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 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 189 GLN ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 677 ASN 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6518 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 10575 Z= 0.252 Angle : 0.598 9.079 14264 Z= 0.312 Chirality : 0.045 0.259 1538 Planarity : 0.004 0.038 1832 Dihedral : 4.475 57.137 1379 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer Outliers : 2.44 % 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: 0.21 (0.24), residues: 1241 helix: 1.01 (0.22), residues: 578 sheet: -0.49 (0.43), residues: 155 loop : -0.57 (0.28), residues: 508 *********************** 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 181 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 153 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 15 residues processed: 165 average time/residue: 1.1393 time to fit residues: 202.9994 Evaluate side-chains 153 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 138 time to evaluate : 1.093 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 8 residues processed: 8 average time/residue: 0.5488 time to fit residues: 6.6133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 0.0670 chunk 93 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 overall best weight: 1.5922 ------------------------------------------------------------------------------- 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 384 ASN ** A 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6532 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 10575 Z= 0.314 Angle : 0.597 8.394 14264 Z= 0.310 Chirality : 0.045 0.230 1538 Planarity : 0.004 0.040 1832 Dihedral : 4.591 60.181 1379 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer Outliers : 3.48 % 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: -0.03 (0.24), residues: 1241 helix: 0.80 (0.22), residues: 587 sheet: -0.48 (0.43), residues: 154 loop : -0.75 (0.27), residues: 500 *********************** 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 182 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 142 time to evaluate : 1.430 Fit side-chains revert: symmetry clash outliers start: 40 outliers final: 20 residues processed: 166 average time/residue: 1.1884 time to fit residues: 213.8681 Evaluate side-chains 155 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 135 time to evaluate : 1.299 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 13 residues processed: 7 average time/residue: 0.5732 time to fit residues: 6.4190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 107 optimal weight: 0.0970 chunk 32 optimal weight: 2.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- 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 380 ASN A 384 ASN ** A 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6522 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.075 10575 Z= 0.273 Angle : 0.563 6.607 14264 Z= 0.294 Chirality : 0.043 0.175 1538 Planarity : 0.004 0.041 1832 Dihedral : 4.560 60.613 1379 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer Outliers : 3.57 % 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: -0.07 (0.24), residues: 1241 helix: 0.74 (0.22), residues: 587 sheet: -0.44 (0.42), residues: 155 loop : -0.76 (0.27), residues: 499 *********************** 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 180 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 139 time to evaluate : 1.288 Fit side-chains revert: symmetry clash outliers start: 41 outliers final: 20 residues processed: 165 average time/residue: 1.1602 time to fit residues: 207.9631 Evaluate side-chains 155 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 135 time to evaluate : 1.576 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 14 residues processed: 6 average time/residue: 0.8697 time to fit residues: 8.1348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 1 optimal weight: 8.9990 chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 0 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 10575 Z= 0.229 Angle : 0.531 6.297 14264 Z= 0.279 Chirality : 0.042 0.179 1538 Planarity : 0.004 0.041 1832 Dihedral : 4.448 60.413 1379 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer Outliers : 3.66 % 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: 0.01 (0.24), residues: 1241 helix: 0.78 (0.22), residues: 589 sheet: -0.40 (0.43), residues: 155 loop : -0.69 (0.28), residues: 497 *********************** 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 189 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 147 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 23 residues processed: 172 average time/residue: 1.1127 time to fit residues: 208.4017 Evaluate side-chains 159 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 136 time to evaluate : 1.287 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 17 residues processed: 6 average time/residue: 0.4650 time to fit residues: 5.3235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 0.2980 chunk 107 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 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 331 ASN ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.6508 moved from start: 0.2932 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= 0.213 Angle : 0.523 6.928 14264 Z= 0.274 Chirality : 0.042 0.186 1538 Planarity : 0.004 0.041 1832 Dihedral : 4.383 60.374 1379 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer Outliers : 3.48 % 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: 0.05 (0.24), residues: 1241 helix: 0.83 (0.22), residues: 589 sheet: -0.44 (0.43), residues: 159 loop : -0.67 (0.27), residues: 493 *********************** 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 179 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 139 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 24 residues processed: 165 average time/residue: 1.1227 time to fit residues: 202.0434 Evaluate side-chains 160 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 136 time to evaluate : 1.098 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 19 residues processed: 5 average time/residue: 0.3117 time to fit residues: 3.5524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 87 optimal weight: 7.9990 chunk 67 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 119 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 457 GLN B 527 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6518 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 10575 Z= 0.257 Angle : 0.550 7.487 14264 Z= 0.287 Chirality : 0.043 0.172 1538 Planarity : 0.004 0.042 1832 Dihedral : 4.471 60.975 1379 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer Outliers : 3.57 % 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: -0.02 (0.24), residues: 1241 helix: 0.77 (0.22), residues: 589 sheet: -0.46 (0.43), residues: 159 loop : -0.71 (0.27), residues: 493 *********************** REFINEMENT MACRO_CYCLE 7 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 180 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 139 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 25 residues processed: 166 average time/residue: 1.1301 time to fit residues: 204.1216 Evaluate side-chains 163 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 138 time to evaluate : 1.217 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 19 residues processed: 6 average time/residue: 0.3118 time to fit residues: 4.2228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 36 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 554 HIS ** A 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.6502 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 10575 Z= 0.199 Angle : 0.529 8.267 14264 Z= 0.277 Chirality : 0.042 0.239 1538 Planarity : 0.004 0.043 1832 Dihedral : 4.382 60.191 1379 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer Outliers : 3.31 % 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: 0.09 (0.24), residues: 1241 helix: 0.89 (0.22), residues: 590 sheet: -0.45 (0.43), residues: 159 loop : -0.68 (0.27), residues: 492 *********************** REFINEMENT MACRO_CYCLE 8 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 176 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 138 time to evaluate : 1.587 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 23 residues processed: 165 average time/residue: 1.1217 time to fit residues: 201.9670 Evaluate side-chains 156 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 133 time to evaluate : 1.191 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 20 residues processed: 3 average time/residue: 0.5611 time to fit residues: 3.6967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 111 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 110 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 ASN B 564 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6516 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 10575 Z= 0.267 Angle : 0.572 8.756 14264 Z= 0.298 Chirality : 0.043 0.240 1538 Planarity : 0.004 0.043 1832 Dihedral : 4.512 61.056 1379 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer Outliers : 2.61 % 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: -0.01 (0.24), residues: 1241 helix: 0.76 (0.22), residues: 588 sheet: -0.38 (0.43), residues: 157 loop : -0.71 (0.27), residues: 496 *********************** REFINEMENT MACRO_CYCLE 9 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 164 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 134 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 23 residues processed: 156 average time/residue: 1.2038 time to fit residues: 204.2548 Evaluate side-chains 155 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 132 time to evaluate : 1.325 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 20 residues processed: 3 average time/residue: 0.9288 time to fit residues: 4.9255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 55 optimal weight: 0.4980 chunk 81 optimal weight: 0.9990 chunk 123 optimal weight: 0.5980 chunk 113 optimal weight: 4.9990 chunk 98 optimal weight: 0.4980 chunk 10 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 760 GLN B 527 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6487 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 10575 Z= 0.172 Angle : 0.514 9.231 14264 Z= 0.270 Chirality : 0.041 0.170 1538 Planarity : 0.004 0.043 1832 Dihedral : 4.285 59.478 1379 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer Outliers : 2.35 % 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: 0.14 (0.24), residues: 1241 helix: 0.95 (0.22), residues: 591 sheet: -0.54 (0.42), residues: 161 loop : -0.64 (0.28), residues: 489 ********************** REFINEMENT MACRO_CYCLE 10 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 166 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 139 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 20 residues processed: 161 average time/residue: 1.2526 time to fit residues: 218.8366 Evaluate side-chains 149 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 129 time to evaluate : 1.209 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 19 residues processed: 1 average time/residue: 0.2772 time to fit residues: 2.1275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 98 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 0.2980 chunk 86 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 760 GLN ** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.195531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.144515 restraints weight = 10914.093| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.23 r_work: 0.3607 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 10575 Z= 0.183 Angle : 0.525 9.408 14264 Z= 0.275 Chirality : 0.041 0.161 1538 Planarity : 0.004 0.043 1832 Dihedral : 4.254 59.375 1379 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer Outliers : 2.35 % 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: 0.17 (0.24), residues: 1241 helix: 0.99 (0.22), residues: 591 sheet: -0.56 (0.42), residues: 166 loop : -0.63 (0.28), residues: 484 =============================================================================== Job complete usr+sys time: 4007.05 seconds wall clock time: 72 minutes 30.93 seconds (4350.93 seconds total)