Starting phenix.real_space_refine on Wed Feb 14 22:06:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gub_34272/02_2024/8gub_34272_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gub_34272/02_2024/8gub_34272.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gub_34272/02_2024/8gub_34272.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gub_34272/02_2024/8gub_34272.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gub_34272/02_2024/8gub_34272_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gub_34272/02_2024/8gub_34272_trim_updated.pdb" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.051 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 73 5.16 5 C 6594 2.51 5 N 1790 2.21 5 O 1898 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 76": "OE1" <-> "OE2" Residue "A PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 538": "OD1" <-> "OD2" Residue "A GLU 674": "OE1" <-> "OE2" Residue "A PHE 794": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 915": "OD1" <-> "OD2" Residue "A TYR 988": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10358 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 977, 7998 Classifications: {'peptide': 977} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 931} Chain breaks: 4 Chain: "B" Number of atoms: 2330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2330 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 271} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'1LT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.41, per 1000 atoms: 0.52 Number of scatterers: 10358 At special positions: 0 Unit cell: (87.822, 119.952, 119.952, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 73 16.00 F 3 9.00 O 1898 8.00 N 1790 7.00 C 6594 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.77 Conformation dependent library (CDL) restraints added in 1.7 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: 2.54 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: 3.05 Time building geometry restraints manager: 4.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1736 1.30 - 1.43: 2686 1.43 - 1.55: 6035 1.55 - 1.68: 6 1.68 - 1.81: 112 Bond restraints: 10575 Sorted by residual: bond pdb=" C9 1LT A1101 " pdb=" S 1LT A1101 " ideal model delta sigma weight residual 1.738 1.521 0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C2 1LT A1101 " pdb=" S 1LT A1101 " ideal model delta sigma weight residual 1.734 1.521 0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" N 1LT A1101 " pdb=" C1 1LT A1101 " ideal model delta sigma weight residual 1.368 1.566 -0.198 2.00e-02 2.50e+03 9.77e+01 bond pdb=" C5 1LT A1101 " pdb=" C6 1LT A1101 " ideal model delta sigma weight residual 1.525 1.351 0.174 2.00e-02 2.50e+03 7.56e+01 bond pdb=" N 1LT A1101 " pdb=" C2 1LT A1101 " ideal model delta sigma weight residual 1.291 1.415 -0.124 2.00e-02 2.50e+03 3.85e+01 ... (remaining 10570 not shown) Histogram of bond angle deviations from ideal: 99.78 - 106.72: 277 106.72 - 113.66: 5970 113.66 - 120.60: 4428 120.60 - 127.53: 3479 127.53 - 134.47: 110 Bond angle restraints: 14264 Sorted by residual: angle pdb=" C2 1LT A1101 " pdb=" S 1LT A1101 " pdb=" C9 1LT A1101 " ideal model delta sigma weight residual 88.90 107.32 -18.42 3.00e+00 1.11e-01 3.77e+01 angle pdb=" N1 1LT A1101 " pdb=" C2 1LT A1101 " pdb=" S 1LT A1101 " ideal model delta sigma weight residual 118.47 134.47 -16.00 3.00e+00 1.11e-01 2.85e+01 angle pdb=" C CYS A 971 " pdb=" N THR A 972 " pdb=" CA THR A 972 " ideal model delta sigma weight residual 120.28 127.27 -6.99 1.34e+00 5.57e-01 2.72e+01 angle pdb=" N 1LT A1101 " pdb=" C2 1LT A1101 " pdb=" N1 1LT A1101 " ideal model delta sigma weight residual 126.74 117.02 9.72 3.00e+00 1.11e-01 1.05e+01 angle pdb=" N 1LT A1101 " pdb=" C1 1LT A1101 " pdb=" C9 1LT A1101 " ideal model delta sigma weight residual 115.40 108.21 7.19 3.00e+00 1.11e-01 5.75e+00 ... (remaining 14259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 5769 17.67 - 35.34: 584 35.34 - 53.01: 95 53.01 - 70.67: 12 70.67 - 88.34: 16 Dihedral angle restraints: 6476 sinusoidal: 2777 harmonic: 3699 Sorted by residual: dihedral pdb=" CA MET A 922 " pdb=" C MET A 922 " pdb=" N VAL A 923 " pdb=" CA VAL A 923 " ideal model delta harmonic sigma weight residual 180.00 -161.21 -18.79 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA GLN B 591 " pdb=" C GLN B 591 " pdb=" N LYS B 592 " pdb=" CA LYS B 592 " ideal model delta harmonic sigma weight residual 180.00 161.76 18.24 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA ASP A 258 " pdb=" C ASP A 258 " pdb=" N GLU A 259 " pdb=" CA GLU A 259 " ideal model delta harmonic sigma weight residual 180.00 162.21 17.79 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 6473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 806 0.028 - 0.056: 482 0.056 - 0.084: 162 0.084 - 0.111: 65 0.111 - 0.139: 23 Chirality restraints: 1538 Sorted by residual: chirality pdb=" CG LEU A 793 " pdb=" CB LEU A 793 " pdb=" CD1 LEU A 793 " pdb=" CD2 LEU A 793 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CA PRO A 562 " pdb=" N PRO A 562 " pdb=" C PRO A 562 " pdb=" CB PRO A 562 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" CA ASN A 918 " pdb=" N ASN A 918 " pdb=" C ASN A 918 " pdb=" CB ASN A 918 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.41e-01 ... (remaining 1535 not shown) Planarity restraints: 1832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 103 " -0.024 5.00e-02 4.00e+02 3.73e-02 2.23e+00 pdb=" N PRO A 104 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 104 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 104 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 538 " 0.023 5.00e-02 4.00e+02 3.48e-02 1.94e+00 pdb=" N PRO A 539 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 539 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 539 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 158 " 0.023 5.00e-02 4.00e+02 3.42e-02 1.87e+00 pdb=" N PRO A 159 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 159 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 159 " 0.019 5.00e-02 4.00e+02 ... (remaining 1829 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.58: 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 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: 0.800 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: 4.080 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 29.010 Find NCS groups from input model: 0.280 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: 0.000 Load rotamer database and sin/cos tables:12.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6272 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.217 10575 Z= 0.531 Angle : 0.620 18.425 14264 Z= 0.304 Chirality : 0.041 0.139 1538 Planarity : 0.003 0.037 1832 Dihedral : 14.425 88.342 4076 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 34.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.17 % Allowed : 0.35 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.24), residues: 1241 helix: 0.70 (0.22), residues: 566 sheet: -1.12 (0.41), residues: 166 loop : -0.75 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 583 HIS 0.004 0.001 HIS A 47 PHE 0.015 0.002 PHE A 667 TYR 0.009 0.001 TYR A 904 ARG 0.007 0.000 ARG A 154 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 199 time to evaluate : 1.307 Fit side-chains revert: symmetry clash REVERT: A 75 GLN cc_start: 0.7141 (mm110) cc_final: 0.6867 (mp-120) REVERT: A 76 GLU cc_start: 0.5684 (mt-10) cc_final: 0.5423 (tm-30) REVERT: A 107 ASN cc_start: 0.6180 (t0) cc_final: 0.5893 (t0) REVERT: A 127 GLU cc_start: 0.6548 (mm-30) cc_final: 0.6303 (mt-10) REVERT: A 130 MET cc_start: 0.6340 (mmm) cc_final: 0.5683 (mmp) REVERT: A 132 LYS cc_start: 0.7135 (mmtm) cc_final: 0.6858 (mptp) REVERT: A 152 ASP cc_start: 0.7107 (m-30) cc_final: 0.6630 (m-30) REVERT: A 164 MET cc_start: 0.6227 (mtt) cc_final: 0.6018 (mtm) REVERT: A 179 LYS cc_start: 0.6408 (tptp) cc_final: 0.6162 (mmmm) REVERT: A 265 TYR cc_start: 0.6397 (m-10) cc_final: 0.5975 (m-10) REVERT: A 282 MET cc_start: 0.6865 (tpp) cc_final: 0.6451 (tpp) REVERT: A 382 ARG cc_start: 0.7778 (ttm-80) cc_final: 0.7552 (ttm-80) REVERT: A 410 LYS cc_start: 0.7177 (tppp) cc_final: 0.6705 (tptp) REVERT: A 453 GLU cc_start: 0.6104 (tt0) cc_final: 0.5445 (tm-30) REVERT: A 579 GLU cc_start: 0.7432 (mm-30) cc_final: 0.6793 (mt-10) REVERT: A 583 MET cc_start: 0.6887 (tpt) cc_final: 0.6499 (tpt) REVERT: A 677 ASN cc_start: 0.7441 (t0) cc_final: 0.6877 (t0) REVERT: A 697 MET cc_start: 0.7032 (tpt) cc_final: 0.6763 (mmp) REVERT: A 732 MET cc_start: 0.6052 (tpt) cc_final: 0.5845 (mmm) REVERT: A 739 MET cc_start: 0.6661 (mtm) cc_final: 0.6424 (mtt) REVERT: A 745 MET cc_start: 0.7042 (tpt) cc_final: 0.6556 (mmm) REVERT: A 772 MET cc_start: 0.6764 (mtp) cc_final: 0.6220 (mtp) REVERT: A 777 ARG cc_start: 0.6237 (mtm110) cc_final: 0.5497 (mmm160) REVERT: A 780 TRP cc_start: 0.7439 (t-100) cc_final: 0.6913 (t-100) REVERT: A 811 MET cc_start: 0.7512 (mtp) cc_final: 0.7239 (mtm) REVERT: A 852 ARG cc_start: 0.6085 (mtm-85) cc_final: 0.5604 (mtm-85) REVERT: A 886 LYS cc_start: 0.7576 (ptpt) cc_final: 0.6687 (pttm) REVERT: A 915 ASP cc_start: 0.7000 (t70) cc_final: 0.6730 (t70) REVERT: A 933 ASP cc_start: 0.7821 (t0) cc_final: 0.6973 (t0) REVERT: A 1010 MET cc_start: 0.7254 (mtm) cc_final: 0.6945 (mtt) REVERT: A 1029 ASP cc_start: 0.7031 (m-30) cc_final: 0.6692 (m-30) REVERT: B 421 ASP cc_start: 0.7794 (t0) cc_final: 0.7383 (m-30) REVERT: B 472 ARG cc_start: 0.6037 (tmm-80) cc_final: 0.5261 (ttm170) REVERT: B 479 MET cc_start: 0.5793 (mtp) cc_final: 0.5360 (mpp) REVERT: B 520 GLU cc_start: 0.7982 (tt0) cc_final: 0.7743 (tm-30) REVERT: B 555 GLU cc_start: 0.6061 (tp30) cc_final: 0.5720 (tt0) REVERT: B 559 ILE cc_start: 0.5862 (mt) cc_final: 0.5526 (mp) outliers start: 2 outliers final: 1 residues processed: 200 average time/residue: 1.2041 time to fit residues: 259.8588 Evaluate side-chains 156 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 155 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 569 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 50 optimal weight: 0.3980 chunk 97 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 879 GLN ** A 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.6236 moved from start: 0.1774 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= 0.210 Angle : 0.565 8.996 14264 Z= 0.294 Chirality : 0.043 0.250 1538 Planarity : 0.004 0.038 1832 Dihedral : 5.964 74.058 1395 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.74 % Allowed : 8.88 % Favored : 89.38 % 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: 0.41 (0.24), residues: 1241 helix: 1.19 (0.22), residues: 576 sheet: -0.47 (0.43), residues: 155 loop : -0.46 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 552 HIS 0.004 0.001 HIS A 362 PHE 0.022 0.002 PHE A 667 TYR 0.014 0.001 TYR A 56 ARG 0.005 0.000 ARG A 79 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 162 time to evaluate : 1.167 Fit side-chains revert: symmetry clash REVERT: A 75 GLN cc_start: 0.7269 (mm110) cc_final: 0.6914 (mp-120) REVERT: A 76 GLU cc_start: 0.5753 (mt-10) cc_final: 0.5390 (mm-30) REVERT: A 127 GLU cc_start: 0.6447 (mm-30) cc_final: 0.6244 (mt-10) REVERT: A 130 MET cc_start: 0.6334 (mmm) cc_final: 0.5682 (mmp) REVERT: A 132 LYS cc_start: 0.7144 (mmtm) cc_final: 0.6934 (mptp) REVERT: A 152 ASP cc_start: 0.7144 (m-30) cc_final: 0.6707 (m-30) REVERT: A 172 GLU cc_start: 0.7062 (mt-10) cc_final: 0.6821 (mt-10) REVERT: A 179 LYS cc_start: 0.6301 (tptp) cc_final: 0.5909 (mmmm) REVERT: A 265 TYR cc_start: 0.6533 (m-10) cc_final: 0.6232 (m-10) REVERT: A 282 MET cc_start: 0.6825 (tpp) cc_final: 0.6377 (tpp) REVERT: A 384 ASN cc_start: 0.7861 (t0) cc_final: 0.6516 (m-40) REVERT: A 441 MET cc_start: 0.7664 (ttm) cc_final: 0.7316 (ttm) REVERT: A 453 GLU cc_start: 0.6188 (tt0) cc_final: 0.5465 (tm-30) REVERT: A 549 ASP cc_start: 0.6017 (t0) cc_final: 0.5590 (m-30) REVERT: A 677 ASN cc_start: 0.7673 (t0) cc_final: 0.7033 (t0) REVERT: A 732 MET cc_start: 0.6185 (tpt) cc_final: 0.5821 (mmm) REVERT: A 734 PHE cc_start: 0.7711 (t80) cc_final: 0.7365 (t80) REVERT: A 738 GLN cc_start: 0.6471 (mm110) cc_final: 0.6046 (mp10) REVERT: A 745 MET cc_start: 0.7369 (tpt) cc_final: 0.6910 (mmm) REVERT: A 746 ASP cc_start: 0.7085 (t0) cc_final: 0.6271 (m-30) REVERT: A 772 MET cc_start: 0.6780 (mtp) cc_final: 0.6538 (mtp) REVERT: A 777 ARG cc_start: 0.6331 (mtm110) cc_final: 0.6042 (mtm-85) REVERT: A 780 TRP cc_start: 0.7559 (t-100) cc_final: 0.7069 (t-100) REVERT: A 794 PHE cc_start: 0.8295 (p90) cc_final: 0.7860 (p90) REVERT: A 825 GLN cc_start: 0.7563 (mm110) cc_final: 0.7329 (mm-40) REVERT: A 852 ARG cc_start: 0.6103 (mtm-85) cc_final: 0.5622 (mtm-85) REVERT: A 886 LYS cc_start: 0.7599 (ptpt) cc_final: 0.6729 (pttm) REVERT: A 933 ASP cc_start: 0.7725 (t0) cc_final: 0.7102 (t70) REVERT: B 421 ASP cc_start: 0.7891 (t0) cc_final: 0.7431 (m-30) REVERT: B 426 TYR cc_start: 0.7335 (m-80) cc_final: 0.7066 (m-80) REVERT: B 472 ARG cc_start: 0.5638 (tmm-80) cc_final: 0.5251 (ttm170) REVERT: B 479 MET cc_start: 0.5789 (mtp) cc_final: 0.5411 (mpp) REVERT: B 520 GLU cc_start: 0.7972 (tt0) cc_final: 0.7406 (pm20) REVERT: B 540 ASP cc_start: 0.5878 (t70) cc_final: 0.5452 (t0) REVERT: B 555 GLU cc_start: 0.5772 (tp30) cc_final: 0.5515 (tt0) REVERT: B 559 ILE cc_start: 0.5433 (mt) cc_final: 0.5194 (mp) outliers start: 20 outliers final: 10 residues processed: 169 average time/residue: 1.2769 time to fit residues: 232.3560 Evaluate side-chains 153 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 143 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 529 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 0.0570 chunk 93 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 chunk 121 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 overall best weight: 1.5302 ------------------------------------------------------------------------------- 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** A 936 HIS ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 GLN B 527 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6262 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 10575 Z= 0.306 Angle : 0.584 8.241 14264 Z= 0.302 Chirality : 0.044 0.235 1538 Planarity : 0.004 0.041 1832 Dihedral : 6.173 80.732 1393 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.79 % Allowed : 12.27 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.24), residues: 1241 helix: 0.88 (0.22), residues: 587 sheet: -0.39 (0.43), residues: 155 loop : -0.70 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 552 HIS 0.004 0.001 HIS A 362 PHE 0.025 0.002 PHE A 667 TYR 0.017 0.002 TYR B 470 ARG 0.005 0.001 ARG A 916 *********************** 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 186 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 154 time to evaluate : 1.239 Fit side-chains revert: symmetry clash REVERT: A 75 GLN cc_start: 0.7292 (mm110) cc_final: 0.6981 (mp-120) REVERT: A 76 GLU cc_start: 0.5904 (mt-10) cc_final: 0.5498 (tm-30) REVERT: A 127 GLU cc_start: 0.6514 (mm-30) cc_final: 0.6229 (mt-10) REVERT: A 179 LYS cc_start: 0.6306 (tptp) cc_final: 0.5908 (mmmm) REVERT: A 249 LYS cc_start: 0.7757 (OUTLIER) cc_final: 0.7163 (tmtt) REVERT: A 265 TYR cc_start: 0.6452 (m-10) cc_final: 0.6149 (m-10) REVERT: A 282 MET cc_start: 0.6776 (tpp) cc_final: 0.6349 (tpp) REVERT: A 384 ASN cc_start: 0.7843 (t0) cc_final: 0.6543 (m-40) REVERT: A 441 MET cc_start: 0.7741 (OUTLIER) cc_final: 0.7396 (ttm) REVERT: A 453 GLU cc_start: 0.6100 (tt0) cc_final: 0.5582 (tm-30) REVERT: A 549 ASP cc_start: 0.6055 (t0) cc_final: 0.5603 (m-30) REVERT: A 677 ASN cc_start: 0.7909 (t0) cc_final: 0.7413 (t0) REVERT: A 732 MET cc_start: 0.6218 (tpt) cc_final: 0.5767 (mmm) REVERT: A 734 PHE cc_start: 0.7575 (t80) cc_final: 0.7209 (t80) REVERT: A 738 GLN cc_start: 0.6464 (mm110) cc_final: 0.5974 (mp10) REVERT: A 739 MET cc_start: 0.8332 (mtt) cc_final: 0.7886 (mtt) REVERT: A 745 MET cc_start: 0.7714 (tpt) cc_final: 0.7189 (mmm) REVERT: A 746 ASP cc_start: 0.7153 (t0) cc_final: 0.6709 (m-30) REVERT: A 768 GLU cc_start: 0.6938 (mm-30) cc_final: 0.6480 (mp0) REVERT: A 772 MET cc_start: 0.6736 (mtp) cc_final: 0.6457 (mtp) REVERT: A 777 ARG cc_start: 0.6384 (mtm110) cc_final: 0.6116 (mtm-85) REVERT: A 794 PHE cc_start: 0.8207 (p90) cc_final: 0.7813 (p90) REVERT: A 822 ASN cc_start: 0.6603 (t0) cc_final: 0.5744 (m-40) REVERT: A 852 ARG cc_start: 0.6153 (mtm-85) cc_final: 0.5881 (mtm-85) REVERT: A 886 LYS cc_start: 0.7497 (ptpt) cc_final: 0.6612 (pttm) REVERT: A 933 ASP cc_start: 0.7934 (t0) cc_final: 0.6956 (t0) REVERT: B 421 ASP cc_start: 0.7894 (t0) cc_final: 0.7529 (m-30) REVERT: B 472 ARG cc_start: 0.5644 (tmm-80) cc_final: 0.5322 (ttm170) REVERT: B 479 MET cc_start: 0.5508 (mtp) cc_final: 0.5136 (mpp) REVERT: B 520 GLU cc_start: 0.7862 (tt0) cc_final: 0.7367 (pm20) REVERT: B 540 ASP cc_start: 0.5816 (t70) cc_final: 0.5391 (t0) REVERT: B 555 GLU cc_start: 0.6055 (tp30) cc_final: 0.5634 (tt0) REVERT: B 559 ILE cc_start: 0.5687 (mt) cc_final: 0.5416 (mp) outliers start: 32 outliers final: 13 residues processed: 171 average time/residue: 1.1732 time to fit residues: 216.8590 Evaluate side-chains 160 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 145 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 412 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 58 optimal weight: 0.0870 chunk 12 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 119 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- 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 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: 0.6232 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10575 Z= 0.183 Angle : 0.507 7.176 14264 Z= 0.264 Chirality : 0.041 0.184 1538 Planarity : 0.004 0.041 1832 Dihedral : 5.968 80.725 1393 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.05 % Allowed : 13.40 % Favored : 83.55 % 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: 0.99 (0.22), residues: 589 sheet: -0.41 (0.42), residues: 160 loop : -0.62 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 552 HIS 0.004 0.001 HIS A 665 PHE 0.021 0.001 PHE A 667 TYR 0.014 0.001 TYR B 470 ARG 0.002 0.000 ARG A 154 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 159 time to evaluate : 1.203 Fit side-chains revert: symmetry clash REVERT: A 75 GLN cc_start: 0.7237 (mm110) cc_final: 0.6895 (mp-120) REVERT: A 76 GLU cc_start: 0.5845 (mt-10) cc_final: 0.5420 (tm-30) REVERT: A 127 GLU cc_start: 0.6579 (mm-30) cc_final: 0.6253 (mt-10) REVERT: A 179 LYS cc_start: 0.6352 (tptp) cc_final: 0.5901 (mmmm) REVERT: A 265 TYR cc_start: 0.6368 (m-10) cc_final: 0.6059 (m-10) REVERT: A 282 MET cc_start: 0.6687 (tpp) cc_final: 0.6354 (tpp) REVERT: A 384 ASN cc_start: 0.7845 (t0) cc_final: 0.6487 (m-40) REVERT: A 404 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7536 (pp) REVERT: A 441 MET cc_start: 0.7690 (ttm) cc_final: 0.7319 (ttm) REVERT: A 453 GLU cc_start: 0.5928 (tt0) cc_final: 0.5495 (tm-30) REVERT: A 549 ASP cc_start: 0.5907 (t0) cc_final: 0.5555 (m-30) REVERT: A 677 ASN cc_start: 0.7882 (t0) cc_final: 0.7350 (t0) REVERT: A 732 MET cc_start: 0.6206 (tpt) cc_final: 0.5802 (mmm) REVERT: A 734 PHE cc_start: 0.7562 (t80) cc_final: 0.7248 (t80) REVERT: A 738 GLN cc_start: 0.6398 (mm110) cc_final: 0.5963 (mp10) REVERT: A 745 MET cc_start: 0.7739 (tpt) cc_final: 0.7259 (mmm) REVERT: A 746 ASP cc_start: 0.7174 (t0) cc_final: 0.6734 (m-30) REVERT: A 768 GLU cc_start: 0.6803 (mm-30) cc_final: 0.6459 (mp0) REVERT: A 780 TRP cc_start: 0.7867 (t-100) cc_final: 0.7204 (t-100) REVERT: A 789 MET cc_start: 0.6872 (mtt) cc_final: 0.6459 (mtm) REVERT: A 794 PHE cc_start: 0.8216 (p90) cc_final: 0.7823 (p90) REVERT: A 822 ASN cc_start: 0.6640 (t0) cc_final: 0.5772 (m-40) REVERT: A 825 GLN cc_start: 0.7576 (mm110) cc_final: 0.7335 (mm110) REVERT: A 886 LYS cc_start: 0.7433 (ptpt) cc_final: 0.6506 (pttm) REVERT: A 933 ASP cc_start: 0.7824 (t0) cc_final: 0.6815 (t0) REVERT: A 956 LEU cc_start: 0.7346 (mt) cc_final: 0.7144 (tp) REVERT: A 976 GLU cc_start: 0.6963 (OUTLIER) cc_final: 0.6717 (pm20) REVERT: B 421 ASP cc_start: 0.7940 (t0) cc_final: 0.7526 (m-30) REVERT: B 426 TYR cc_start: 0.7285 (m-80) cc_final: 0.7020 (m-80) REVERT: B 472 ARG cc_start: 0.5654 (tmm-80) cc_final: 0.5435 (ttm170) REVERT: B 479 MET cc_start: 0.5525 (mtp) cc_final: 0.5135 (mpp) REVERT: B 520 GLU cc_start: 0.7846 (tt0) cc_final: 0.7318 (pm20) REVERT: B 540 ASP cc_start: 0.5746 (t70) cc_final: 0.5373 (t0) REVERT: B 547 GLU cc_start: 0.6486 (mm-30) cc_final: 0.5986 (mt-10) REVERT: B 555 GLU cc_start: 0.6225 (tp30) cc_final: 0.5804 (tt0) REVERT: B 559 ILE cc_start: 0.5589 (mt) cc_final: 0.5331 (mp) outliers start: 35 outliers final: 19 residues processed: 180 average time/residue: 1.1960 time to fit residues: 232.4528 Evaluate side-chains 174 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 153 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 922 MET Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 976 GLU Chi-restraints excluded: chain A residue 993 GLN Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 580 TYR 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: 1.9990 chunk 1 optimal weight: 7.9990 chunk 89 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 102 optimal weight: 0.2980 chunk 82 optimal weight: 0.5980 chunk 0 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.6229 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10575 Z= 0.186 Angle : 0.501 6.735 14264 Z= 0.260 Chirality : 0.041 0.184 1538 Planarity : 0.004 0.042 1832 Dihedral : 5.914 80.721 1393 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.96 % Allowed : 14.36 % Favored : 82.68 % 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: 0.32 (0.24), residues: 1241 helix: 1.05 (0.22), residues: 584 sheet: -0.31 (0.42), residues: 158 loop : -0.52 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 552 HIS 0.004 0.001 HIS A 665 PHE 0.021 0.001 PHE A 667 TYR 0.020 0.001 TYR A 182 ARG 0.002 0.000 ARG A 154 *********************** 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: 34 poor density : 155 time to evaluate : 1.211 Fit side-chains revert: symmetry clash REVERT: A 39 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6696 (mp0) REVERT: A 75 GLN cc_start: 0.7243 (mm110) cc_final: 0.6904 (mp-120) REVERT: A 76 GLU cc_start: 0.5943 (mt-10) cc_final: 0.5496 (tm-30) REVERT: A 83 PHE cc_start: 0.7338 (m-80) cc_final: 0.6972 (m-80) REVERT: A 127 GLU cc_start: 0.6602 (mm-30) cc_final: 0.6256 (mt-10) REVERT: A 172 GLU cc_start: 0.7202 (mt-10) cc_final: 0.6984 (mt-10) REVERT: A 179 LYS cc_start: 0.6349 (tptp) cc_final: 0.5890 (mmmm) REVERT: A 265 TYR cc_start: 0.6373 (m-10) cc_final: 0.6061 (m-10) REVERT: A 282 MET cc_start: 0.6659 (tpp) cc_final: 0.6320 (tpp) REVERT: A 384 ASN cc_start: 0.7834 (t0) cc_final: 0.6481 (m-40) REVERT: A 404 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7526 (pp) REVERT: A 441 MET cc_start: 0.7746 (ttm) cc_final: 0.7388 (ttm) REVERT: A 453 GLU cc_start: 0.5959 (tt0) cc_final: 0.5521 (tm-30) REVERT: A 549 ASP cc_start: 0.5858 (t0) cc_final: 0.5522 (m-30) REVERT: A 677 ASN cc_start: 0.7882 (t0) cc_final: 0.7452 (t0) REVERT: A 732 MET cc_start: 0.6186 (tpt) cc_final: 0.5800 (mmm) REVERT: A 734 PHE cc_start: 0.7599 (t80) cc_final: 0.7245 (t80) REVERT: A 738 GLN cc_start: 0.6382 (mm110) cc_final: 0.5882 (mp10) REVERT: A 739 MET cc_start: 0.8299 (mtt) cc_final: 0.8089 (mtt) REVERT: A 745 MET cc_start: 0.7704 (tpt) cc_final: 0.7187 (mmm) REVERT: A 746 ASP cc_start: 0.7136 (t0) cc_final: 0.6688 (m-30) REVERT: A 768 GLU cc_start: 0.6898 (mm-30) cc_final: 0.6546 (mp0) REVERT: A 780 TRP cc_start: 0.7839 (t-100) cc_final: 0.7196 (t-100) REVERT: A 789 MET cc_start: 0.6850 (mtt) cc_final: 0.6488 (mtm) REVERT: A 794 PHE cc_start: 0.8183 (p90) cc_final: 0.7796 (p90) REVERT: A 822 ASN cc_start: 0.6651 (t0) cc_final: 0.5785 (m-40) REVERT: A 825 GLN cc_start: 0.7681 (mm110) cc_final: 0.7395 (mm110) REVERT: A 886 LYS cc_start: 0.7438 (ptpt) cc_final: 0.6518 (pttm) REVERT: A 933 ASP cc_start: 0.7815 (t0) cc_final: 0.6795 (t0) REVERT: A 1029 ASP cc_start: 0.6923 (m-30) cc_final: 0.6512 (m-30) REVERT: B 364 MET cc_start: 0.5575 (OUTLIER) cc_final: 0.5041 (tmt) REVERT: B 421 ASP cc_start: 0.7890 (t0) cc_final: 0.7592 (m-30) REVERT: B 426 TYR cc_start: 0.7259 (m-80) cc_final: 0.7033 (m-80) REVERT: B 472 ARG cc_start: 0.5573 (tmm-80) cc_final: 0.5349 (ttm170) REVERT: B 479 MET cc_start: 0.5416 (mtp) cc_final: 0.5032 (mpp) REVERT: B 520 GLU cc_start: 0.7805 (tt0) cc_final: 0.7277 (pm20) REVERT: B 540 ASP cc_start: 0.5819 (t70) cc_final: 0.5432 (t0) REVERT: B 547 GLU cc_start: 0.6397 (mm-30) cc_final: 0.5947 (mt-10) REVERT: B 555 GLU cc_start: 0.6238 (tp30) cc_final: 0.5812 (tt0) REVERT: B 559 ILE cc_start: 0.5525 (mt) cc_final: 0.5292 (mp) outliers start: 34 outliers final: 19 residues processed: 172 average time/residue: 1.1405 time to fit residues: 213.2729 Evaluate side-chains 171 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 149 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 993 GLN Chi-restraints excluded: chain B residue 364 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 chunk 99 optimal weight: 0.3980 chunk 55 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 931 HIS ** 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: 0.6225 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10575 Z= 0.181 Angle : 0.492 6.915 14264 Z= 0.255 Chirality : 0.040 0.167 1538 Planarity : 0.004 0.042 1832 Dihedral : 5.870 80.378 1393 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.39 % Allowed : 15.23 % Favored : 81.38 % 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: 1.04 (0.22), residues: 590 sheet: -0.44 (0.42), residues: 163 loop : -0.54 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 552 HIS 0.003 0.001 HIS A 665 PHE 0.020 0.001 PHE A 667 TYR 0.019 0.001 TYR A 182 ARG 0.002 0.000 ARG A 154 *********************** 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 190 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 151 time to evaluate : 1.326 Fit side-chains revert: symmetry clash REVERT: A 39 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.6692 (mp0) REVERT: A 75 GLN cc_start: 0.7277 (mm110) cc_final: 0.6937 (mp-120) REVERT: A 76 GLU cc_start: 0.5814 (mt-10) cc_final: 0.5377 (tm-30) REVERT: A 127 GLU cc_start: 0.6620 (mm-30) cc_final: 0.6260 (mt-10) REVERT: A 172 GLU cc_start: 0.7194 (mt-10) cc_final: 0.6972 (mt-10) REVERT: A 179 LYS cc_start: 0.6339 (tptp) cc_final: 0.5881 (mmmm) REVERT: A 249 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.7107 (tmtt) REVERT: A 265 TYR cc_start: 0.6338 (m-10) cc_final: 0.6038 (m-10) REVERT: A 282 MET cc_start: 0.6650 (tpp) cc_final: 0.6306 (tpp) REVERT: A 384 ASN cc_start: 0.7817 (t0) cc_final: 0.6459 (m-40) REVERT: A 404 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7510 (pp) REVERT: A 441 MET cc_start: 0.7753 (ttm) cc_final: 0.7415 (ttm) REVERT: A 453 GLU cc_start: 0.5941 (tt0) cc_final: 0.5527 (tm-30) REVERT: A 549 ASP cc_start: 0.5954 (t0) cc_final: 0.5553 (m-30) REVERT: A 621 LYS cc_start: 0.7145 (ptpt) cc_final: 0.6546 (ptpp) REVERT: A 677 ASN cc_start: 0.7829 (t0) cc_final: 0.7473 (t0) REVERT: A 732 MET cc_start: 0.6175 (tpt) cc_final: 0.5790 (mmm) REVERT: A 745 MET cc_start: 0.7692 (tpt) cc_final: 0.7205 (mmm) REVERT: A 746 ASP cc_start: 0.7130 (t0) cc_final: 0.6704 (m-30) REVERT: A 768 GLU cc_start: 0.6883 (mm-30) cc_final: 0.6525 (mp0) REVERT: A 780 TRP cc_start: 0.7794 (t-100) cc_final: 0.7168 (t-100) REVERT: A 789 MET cc_start: 0.6871 (mtt) cc_final: 0.6410 (mtm) REVERT: A 822 ASN cc_start: 0.6665 (t0) cc_final: 0.5788 (m-40) REVERT: A 825 GLN cc_start: 0.7627 (mm110) cc_final: 0.7408 (mm110) REVERT: A 886 LYS cc_start: 0.7450 (ptpt) cc_final: 0.6535 (pttm) REVERT: A 933 ASP cc_start: 0.7823 (t0) cc_final: 0.6796 (t0) REVERT: A 1029 ASP cc_start: 0.6924 (m-30) cc_final: 0.6514 (m-30) REVERT: B 364 MET cc_start: 0.5555 (OUTLIER) cc_final: 0.5150 (tmt) REVERT: B 421 ASP cc_start: 0.7839 (t0) cc_final: 0.7576 (m-30) REVERT: B 479 MET cc_start: 0.5404 (mtp) cc_final: 0.5020 (mpp) REVERT: B 520 GLU cc_start: 0.7785 (tt0) cc_final: 0.7174 (pm20) REVERT: B 540 ASP cc_start: 0.5780 (t70) cc_final: 0.5390 (t0) REVERT: B 547 GLU cc_start: 0.6355 (mm-30) cc_final: 0.5928 (mt-10) REVERT: B 555 GLU cc_start: 0.6369 (tp30) cc_final: 0.5927 (tt0) REVERT: B 559 ILE cc_start: 0.5529 (mt) cc_final: 0.5268 (mp) outliers start: 39 outliers final: 21 residues processed: 175 average time/residue: 1.1085 time to fit residues: 210.4592 Evaluate side-chains 171 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 146 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 993 GLN Chi-restraints excluded: chain B residue 364 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 68 optimal weight: 0.0980 chunk 87 optimal weight: 5.9990 chunk 67 optimal weight: 0.3980 chunk 100 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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** ** 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: 0.6258 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 10575 Z= 0.323 Angle : 0.585 7.599 14264 Z= 0.299 Chirality : 0.045 0.241 1538 Planarity : 0.004 0.043 1832 Dihedral : 6.269 85.688 1393 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.48 % Allowed : 16.19 % Favored : 80.33 % 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: 586 sheet: -0.37 (0.43), residues: 156 loop : -0.68 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 552 HIS 0.005 0.001 HIS A 362 PHE 0.024 0.002 PHE A 794 TYR 0.020 0.002 TYR A 182 ARG 0.004 0.001 ARG A 154 *********************** 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 188 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 148 time to evaluate : 1.283 Fit side-chains revert: symmetry clash REVERT: A 39 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6695 (mp0) REVERT: A 75 GLN cc_start: 0.7372 (mm110) cc_final: 0.7015 (mp-120) REVERT: A 76 GLU cc_start: 0.6000 (mt-10) cc_final: 0.5561 (tm-30) REVERT: A 83 PHE cc_start: 0.7304 (m-80) cc_final: 0.6974 (m-80) REVERT: A 127 GLU cc_start: 0.6594 (mm-30) cc_final: 0.6215 (mt-10) REVERT: A 179 LYS cc_start: 0.6328 (tptp) cc_final: 0.5864 (mmmm) REVERT: A 249 LYS cc_start: 0.7739 (OUTLIER) cc_final: 0.7157 (tmtt) REVERT: A 265 TYR cc_start: 0.6349 (m-10) cc_final: 0.6053 (m-10) REVERT: A 282 MET cc_start: 0.6669 (tpp) cc_final: 0.6319 (tpp) REVERT: A 352 ASP cc_start: 0.7444 (OUTLIER) cc_final: 0.7070 (m-30) REVERT: A 404 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7610 (pp) REVERT: A 441 MET cc_start: 0.7733 (ttm) cc_final: 0.7413 (ttm) REVERT: A 453 GLU cc_start: 0.5994 (tt0) cc_final: 0.5536 (tm-30) REVERT: A 549 ASP cc_start: 0.5869 (t0) cc_final: 0.5505 (m-30) REVERT: A 561 ILE cc_start: 0.7464 (OUTLIER) cc_final: 0.7238 (mp) REVERT: A 677 ASN cc_start: 0.7961 (t0) cc_final: 0.7554 (t0) REVERT: A 732 MET cc_start: 0.6248 (tpt) cc_final: 0.5901 (mmm) REVERT: A 745 MET cc_start: 0.7684 (tpt) cc_final: 0.7217 (mmm) REVERT: A 768 GLU cc_start: 0.6895 (mm-30) cc_final: 0.6576 (mp0) REVERT: A 780 TRP cc_start: 0.7775 (t-100) cc_final: 0.7170 (t-100) REVERT: A 822 ASN cc_start: 0.6704 (t0) cc_final: 0.5856 (m-40) REVERT: A 886 LYS cc_start: 0.7446 (ptpt) cc_final: 0.6522 (pttm) REVERT: A 933 ASP cc_start: 0.7810 (t0) cc_final: 0.6848 (t0) REVERT: A 1029 ASP cc_start: 0.6952 (m-30) cc_final: 0.6531 (m-30) REVERT: B 421 ASP cc_start: 0.7859 (t0) cc_final: 0.7583 (m-30) REVERT: B 479 MET cc_start: 0.5426 (mtp) cc_final: 0.5030 (mpp) REVERT: B 520 GLU cc_start: 0.7789 (tt0) cc_final: 0.7187 (pm20) REVERT: B 540 ASP cc_start: 0.5828 (t70) cc_final: 0.5416 (t0) REVERT: B 555 GLU cc_start: 0.6387 (tp30) cc_final: 0.5835 (tt0) REVERT: B 559 ILE cc_start: 0.5506 (mt) cc_final: 0.5240 (mp) outliers start: 40 outliers final: 22 residues processed: 171 average time/residue: 1.0878 time to fit residues: 201.8674 Evaluate side-chains 176 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 149 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 993 GLN Chi-restraints excluded: chain B residue 364 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 71 optimal weight: 0.4980 chunk 36 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 11 optimal weight: 0.4980 chunk 93 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 ** 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: 0.6237 moved from start: 0.2891 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 : 0.528 8.211 14264 Z= 0.273 Chirality : 0.042 0.157 1538 Planarity : 0.004 0.043 1832 Dihedral : 6.200 88.823 1393 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.48 % Allowed : 16.19 % Favored : 80.33 % 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: 0.12 (0.24), residues: 1241 helix: 0.87 (0.22), residues: 588 sheet: -0.31 (0.43), residues: 157 loop : -0.65 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 552 HIS 0.004 0.001 HIS A 450 PHE 0.021 0.001 PHE A 667 TYR 0.016 0.001 TYR B 470 ARG 0.002 0.000 ARG A 916 *********************** 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 188 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 148 time to evaluate : 1.241 Fit side-chains revert: symmetry clash REVERT: A 39 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6684 (mp0) REVERT: A 75 GLN cc_start: 0.7291 (mm110) cc_final: 0.6965 (mp-120) REVERT: A 76 GLU cc_start: 0.5819 (mt-10) cc_final: 0.5390 (tm-30) REVERT: A 127 GLU cc_start: 0.6594 (mm-30) cc_final: 0.6207 (mt-10) REVERT: A 179 LYS cc_start: 0.6407 (tptp) cc_final: 0.5864 (mmmm) REVERT: A 265 TYR cc_start: 0.6303 (m-10) cc_final: 0.5989 (m-10) REVERT: A 282 MET cc_start: 0.6655 (tpp) cc_final: 0.6304 (tpp) REVERT: A 352 ASP cc_start: 0.7423 (OUTLIER) cc_final: 0.7066 (m-30) REVERT: A 404 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7579 (pp) REVERT: A 441 MET cc_start: 0.7759 (OUTLIER) cc_final: 0.7453 (ttm) REVERT: A 453 GLU cc_start: 0.5964 (tt0) cc_final: 0.5504 (tm-30) REVERT: A 549 ASP cc_start: 0.5823 (t0) cc_final: 0.5476 (m-30) REVERT: A 677 ASN cc_start: 0.7905 (t0) cc_final: 0.7529 (t0) REVERT: A 732 MET cc_start: 0.6265 (tpt) cc_final: 0.5909 (mmm) REVERT: A 745 MET cc_start: 0.7633 (tpt) cc_final: 0.7176 (mmm) REVERT: A 746 ASP cc_start: 0.7379 (t0) cc_final: 0.6904 (m-30) REVERT: A 768 GLU cc_start: 0.6870 (mm-30) cc_final: 0.6546 (mp0) REVERT: A 780 TRP cc_start: 0.7740 (t-100) cc_final: 0.7140 (t-100) REVERT: A 789 MET cc_start: 0.6878 (mtt) cc_final: 0.6476 (mtt) REVERT: A 822 ASN cc_start: 0.6683 (t0) cc_final: 0.5817 (m-40) REVERT: A 825 GLN cc_start: 0.7583 (mm110) cc_final: 0.7375 (mm-40) REVERT: A 886 LYS cc_start: 0.7431 (ptpt) cc_final: 0.6488 (pttm) REVERT: A 933 ASP cc_start: 0.7837 (t0) cc_final: 0.6820 (t0) REVERT: A 1029 ASP cc_start: 0.6948 (m-30) cc_final: 0.6538 (m-30) REVERT: B 364 MET cc_start: 0.5673 (OUTLIER) cc_final: 0.5140 (tmt) REVERT: B 421 ASP cc_start: 0.7807 (t0) cc_final: 0.7601 (m-30) REVERT: B 479 MET cc_start: 0.5605 (mtp) cc_final: 0.5168 (mpp) REVERT: B 520 GLU cc_start: 0.7684 (tt0) cc_final: 0.7146 (pm20) REVERT: B 540 ASP cc_start: 0.5843 (t70) cc_final: 0.5424 (t0) REVERT: B 555 GLU cc_start: 0.6352 (tp30) cc_final: 0.5812 (tt0) REVERT: B 559 ILE cc_start: 0.5568 (mt) cc_final: 0.5328 (mp) outliers start: 40 outliers final: 24 residues processed: 173 average time/residue: 1.1445 time to fit residues: 214.8059 Evaluate side-chains 174 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 145 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 976 GLU Chi-restraints excluded: chain A residue 993 GLN Chi-restraints excluded: chain B residue 364 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 5.9990 chunk 104 optimal weight: 0.4980 chunk 111 optimal weight: 0.9990 chunk 67 optimal weight: 0.2980 chunk 48 optimal weight: 1.9990 chunk 87 optimal weight: 0.0670 chunk 34 optimal weight: 0.3980 chunk 100 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 110 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 overall best weight: 0.4520 ------------------------------------------------------------------------------- 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** ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 ASN B 564 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6208 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10575 Z= 0.149 Angle : 0.490 8.912 14264 Z= 0.254 Chirality : 0.040 0.181 1538 Planarity : 0.004 0.044 1832 Dihedral : 6.075 89.629 1393 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.52 % Allowed : 17.06 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.24), residues: 1241 helix: 1.06 (0.22), residues: 589 sheet: -0.32 (0.43), residues: 161 loop : -0.56 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 552 HIS 0.005 0.001 HIS A 554 PHE 0.027 0.001 PHE A 794 TYR 0.013 0.001 TYR A 904 ARG 0.003 0.000 ARG A 38 *********************** 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 179 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 150 time to evaluate : 1.114 Fit side-chains revert: symmetry clash REVERT: A 39 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6679 (mp0) REVERT: A 75 GLN cc_start: 0.7332 (mm110) cc_final: 0.6993 (mp-120) REVERT: A 76 GLU cc_start: 0.5807 (mt-10) cc_final: 0.5369 (tm-30) REVERT: A 127 GLU cc_start: 0.6596 (mm-30) cc_final: 0.6213 (mt-10) REVERT: A 179 LYS cc_start: 0.6402 (tptp) cc_final: 0.5853 (mmmm) REVERT: A 265 TYR cc_start: 0.6232 (m-10) cc_final: 0.5903 (m-10) REVERT: A 282 MET cc_start: 0.6653 (tpp) cc_final: 0.6287 (tpp) REVERT: A 332 SER cc_start: 0.7778 (m) cc_final: 0.7458 (t) REVERT: A 441 MET cc_start: 0.7763 (ttm) cc_final: 0.7441 (ttm) REVERT: A 453 GLU cc_start: 0.5784 (tt0) cc_final: 0.5367 (tm-30) REVERT: A 621 LYS cc_start: 0.7107 (ptpt) cc_final: 0.6662 (ptpp) REVERT: A 677 ASN cc_start: 0.7782 (t0) cc_final: 0.7430 (t0) REVERT: A 732 MET cc_start: 0.6225 (tpt) cc_final: 0.5917 (mmm) REVERT: A 745 MET cc_start: 0.7628 (tpt) cc_final: 0.7159 (mmm) REVERT: A 746 ASP cc_start: 0.7257 (t0) cc_final: 0.6761 (m-30) REVERT: A 768 GLU cc_start: 0.6878 (mm-30) cc_final: 0.6533 (mp0) REVERT: A 777 ARG cc_start: 0.6290 (mtm110) cc_final: 0.6083 (mtm-85) REVERT: A 780 TRP cc_start: 0.7666 (t-100) cc_final: 0.7074 (t-100) REVERT: A 789 MET cc_start: 0.6650 (mtt) cc_final: 0.6257 (mtt) REVERT: A 822 ASN cc_start: 0.6671 (t0) cc_final: 0.5776 (m-40) REVERT: A 886 LYS cc_start: 0.7409 (ptpt) cc_final: 0.6488 (pttm) REVERT: A 933 ASP cc_start: 0.7810 (t0) cc_final: 0.6790 (t0) REVERT: A 1029 ASP cc_start: 0.6914 (m-30) cc_final: 0.6507 (m-30) REVERT: B 364 MET cc_start: 0.5563 (OUTLIER) cc_final: 0.5318 (mtt) REVERT: B 479 MET cc_start: 0.5532 (mtp) cc_final: 0.5118 (mpp) REVERT: B 520 GLU cc_start: 0.7658 (tt0) cc_final: 0.7153 (pm20) REVERT: B 540 ASP cc_start: 0.5759 (t70) cc_final: 0.5378 (t0) REVERT: B 555 GLU cc_start: 0.6456 (tp30) cc_final: 0.5950 (tt0) REVERT: B 559 ILE cc_start: 0.5762 (mt) cc_final: 0.5529 (mp) outliers start: 29 outliers final: 21 residues processed: 168 average time/residue: 1.1035 time to fit residues: 202.3847 Evaluate side-chains 166 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 143 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 993 GLN Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 422 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 9.9990 chunk 71 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 chunk 113 optimal weight: 0.5980 chunk 98 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 879 GLN ** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6219 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10575 Z= 0.181 Angle : 0.516 9.253 14264 Z= 0.267 Chirality : 0.041 0.189 1538 Planarity : 0.004 0.044 1832 Dihedral : 5.965 85.978 1393 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.52 % Allowed : 18.02 % Favored : 79.46 % 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: 1.04 (0.22), residues: 589 sheet: -0.33 (0.43), residues: 161 loop : -0.58 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 552 HIS 0.004 0.001 HIS A 554 PHE 0.021 0.001 PHE A 667 TYR 0.015 0.001 TYR A 432 ARG 0.002 0.000 ARG A 382 ********************** 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 170 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 141 time to evaluate : 1.256 Fit side-chains revert: symmetry clash REVERT: A 39 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6649 (mp0) REVERT: A 75 GLN cc_start: 0.7324 (mm110) cc_final: 0.6967 (mp-120) REVERT: A 76 GLU cc_start: 0.5818 (mt-10) cc_final: 0.5373 (tm-30) REVERT: A 127 GLU cc_start: 0.6594 (mm-30) cc_final: 0.6215 (mt-10) REVERT: A 179 LYS cc_start: 0.6408 (tptp) cc_final: 0.5861 (mmmm) REVERT: A 265 TYR cc_start: 0.6260 (m-10) cc_final: 0.5941 (m-10) REVERT: A 282 MET cc_start: 0.6651 (tpp) cc_final: 0.6287 (tpp) REVERT: A 332 SER cc_start: 0.7786 (m) cc_final: 0.7451 (t) REVERT: A 441 MET cc_start: 0.7809 (ttm) cc_final: 0.7486 (ttm) REVERT: A 453 GLU cc_start: 0.5934 (tt0) cc_final: 0.5523 (tm-30) REVERT: A 677 ASN cc_start: 0.7785 (t0) cc_final: 0.7435 (t0) REVERT: A 732 MET cc_start: 0.6210 (tpt) cc_final: 0.5901 (mmm) REVERT: A 745 MET cc_start: 0.7634 (tpt) cc_final: 0.7157 (mmm) REVERT: A 746 ASP cc_start: 0.7266 (t0) cc_final: 0.6769 (m-30) REVERT: A 768 GLU cc_start: 0.6876 (mm-30) cc_final: 0.6589 (mp0) REVERT: A 777 ARG cc_start: 0.6294 (mtm110) cc_final: 0.6087 (mtm-85) REVERT: A 780 TRP cc_start: 0.7614 (t-100) cc_final: 0.7042 (t-100) REVERT: A 789 MET cc_start: 0.6867 (mtt) cc_final: 0.6443 (mtt) REVERT: A 822 ASN cc_start: 0.6698 (t0) cc_final: 0.5806 (m-40) REVERT: A 886 LYS cc_start: 0.7416 (ptpt) cc_final: 0.6494 (pttm) REVERT: A 933 ASP cc_start: 0.7840 (t0) cc_final: 0.6805 (t0) REVERT: A 1029 ASP cc_start: 0.6913 (m-30) cc_final: 0.6503 (m-30) REVERT: B 364 MET cc_start: 0.5570 (OUTLIER) cc_final: 0.5331 (mtt) REVERT: B 479 MET cc_start: 0.5547 (mtp) cc_final: 0.5131 (mpp) REVERT: B 520 GLU cc_start: 0.7569 (tt0) cc_final: 0.7102 (pm20) REVERT: B 540 ASP cc_start: 0.5730 (t70) cc_final: 0.5331 (t0) REVERT: B 555 GLU cc_start: 0.6457 (tp30) cc_final: 0.5935 (tt0) REVERT: B 559 ILE cc_start: 0.5775 (mt) cc_final: 0.5540 (mp) outliers start: 29 outliers final: 23 residues processed: 158 average time/residue: 1.0533 time to fit residues: 181.2008 Evaluate side-chains 164 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 139 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 993 GLN Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 422 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 90 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN A 296 GLN ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 879 GLN B 527 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.195817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.146286 restraints weight = 10945.007| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 2.04 r_work: 0.3544 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10575 Z= 0.195 Angle : 0.523 9.195 14264 Z= 0.271 Chirality : 0.041 0.185 1538 Planarity : 0.004 0.044 1832 Dihedral : 5.686 76.878 1393 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.44 % Allowed : 17.93 % Favored : 79.63 % 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: 0.27 (0.24), residues: 1241 helix: 1.03 (0.22), residues: 589 sheet: -0.34 (0.42), residues: 161 loop : -0.58 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 583 HIS 0.004 0.001 HIS A 554 PHE 0.021 0.001 PHE A 667 TYR 0.015 0.001 TYR B 470 ARG 0.002 0.000 ARG A 382 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4141.22 seconds wall clock time: 74 minutes 24.69 seconds (4464.69 seconds total)