Starting phenix.real_space_refine on Mon Mar 18 17:57:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m69_23691/03_2024/7m69_23691_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m69_23691/03_2024/7m69_23691.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m69_23691/03_2024/7m69_23691.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m69_23691/03_2024/7m69_23691.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m69_23691/03_2024/7m69_23691_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m69_23691/03_2024/7m69_23691_trim_updated.pdb" } resolution = 3.42 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= 0.758 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 S 47 5.16 5 C 7028 2.51 5 N 1824 2.21 5 O 1981 1.98 5 H 10898 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21781 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 21781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1390, 21781 Classifications: {'peptide': 1390} Link IDs: {'PTRANS': 37, 'TRANS': 1352} Chain breaks: 4 Unresolved non-hydrogen bonds: 225 Unresolved non-hydrogen angles: 283 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 4, 'TPO:plan-1': 1, 'TYR:plan': 4, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 141 Time building chain proxies: 9.80, per 1000 atoms: 0.45 Number of scatterers: 21781 At special positions: 0 Unit cell: (129.906, 123.72, 107.224, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 47 16.00 P 3 15.00 O 1981 8.00 N 1824 7.00 C 7028 6.00 H 10898 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 946 " - pdb=" SG CYS A1017 " distance=2.02 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: 17.65 Conformation dependent library (CDL) restraints added in 2.2 seconds 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2632 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 5 sheets defined 63.8% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.02 Creating SS restraints... Processing helix chain 'A' and resid 30 through 59 removed outlier: 4.902A pdb=" N LEU A 53 " --> pdb=" O GLY A 49 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N VAL A 54 " --> pdb=" O ILE A 50 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN A 55 " --> pdb=" O ARG A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 97 removed outlier: 3.566A pdb=" N ILE A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N SER A 94 " --> pdb=" O SER A 90 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N GLU A 97 " --> pdb=" O ILE A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 123 removed outlier: 3.779A pdb=" N LEU A 118 " --> pdb=" O LEU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 158 Processing helix chain 'A' and resid 168 through 188 removed outlier: 3.835A pdb=" N ILE A 171 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 174 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE A 178 " --> pdb=" O PHE A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 201 removed outlier: 3.685A pdb=" N HIS A 201 " --> pdb=" O GLN A 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 198 through 201' Processing helix chain 'A' and resid 217 through 222 removed outlier: 3.808A pdb=" N THR A 222 " --> pdb=" O PHE A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 235 removed outlier: 3.816A pdb=" N GLY A 228 " --> pdb=" O TRP A 225 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU A 235 " --> pdb=" O THR A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 268 removed outlier: 3.616A pdb=" N ASN A 262 " --> pdb=" O LYS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 283 removed outlier: 3.896A pdb=" N LEU A 275 " --> pdb=" O ASN A 272 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG A 281 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE A 283 " --> pdb=" O CYS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 327 removed outlier: 3.996A pdb=" N LEU A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) Proline residue: A 305 - end of helix Processing helix chain 'A' and resid 343 through 390 removed outlier: 3.679A pdb=" N ALA A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR A 386 " --> pdb=" O THR A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 399 Processing helix chain 'A' and resid 402 through 410 removed outlier: 3.903A pdb=" N MET A 409 " --> pdb=" O ILE A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 421 removed outlier: 3.884A pdb=" N GLN A 421 " --> pdb=" O GLN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 444 Proline residue: A 430 - end of helix Processing helix chain 'A' and resid 450 through 492 Proline residue: A 460 - end of helix removed outlier: 3.679A pdb=" N ARG A 467 " --> pdb=" O SER A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 500 Processing helix chain 'A' and resid 504 through 554 removed outlier: 4.337A pdb=" N CYS A 527 " --> pdb=" O THR A 523 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER A 533 " --> pdb=" O MET A 529 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE A 534 " --> pdb=" O ALA A 530 " (cutoff:3.500A) Proline residue: A 540 - end of helix Processing helix chain 'A' and resid 564 through 602 removed outlier: 3.666A pdb=" N SER A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N PHE A 576 " --> pdb=" O ASN A 572 " (cutoff:3.500A) Proline residue: A 577 - end of helix removed outlier: 3.545A pdb=" N ILE A 580 " --> pdb=" O PHE A 576 " (cutoff:3.500A) Proline residue: A 582 - end of helix removed outlier: 3.746A pdb=" N LEU A 585 " --> pdb=" O ILE A 581 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASN A 586 " --> pdb=" O PRO A 582 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A 587 " --> pdb=" O MET A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 677 Processing helix chain 'A' and resid 707 through 712 Processing helix chain 'A' and resid 719 through 728 Processing helix chain 'A' and resid 732 through 738 removed outlier: 4.666A pdb=" N LEU A 738 " --> pdb=" O ASP A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 768 Processing helix chain 'A' and resid 785 through 796 removed outlier: 4.024A pdb=" N GLU A 793 " --> pdb=" O ARG A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 819 Processing helix chain 'A' and resid 837 through 842 Processing helix chain 'A' and resid 921 through 928 Processing helix chain 'A' and resid 937 through 945 Processing helix chain 'A' and resid 948 through 981 removed outlier: 3.808A pdb=" N CYS A 952 " --> pdb=" O PRO A 948 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL A 953 " --> pdb=" O LYS A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 1034 removed outlier: 4.064A pdb=" N TRP A1014 " --> pdb=" O THR A1010 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR A1018 " --> pdb=" O TRP A1014 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ILE A1019 " --> pdb=" O VAL A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1043 Processing helix chain 'A' and resid 1046 through 1059 removed outlier: 3.560A pdb=" N ILE A1057 " --> pdb=" O PHE A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1087 Processing helix chain 'A' and resid 1093 through 1137 Proline residue: A1098 - end of helix removed outlier: 4.025A pdb=" N ARG A1115 " --> pdb=" O LEU A1111 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLU A1116 " --> pdb=" O ARG A1112 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG A1125 " --> pdb=" O ASP A1121 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N SER A1126 " --> pdb=" O SER A1122 " (cutoff:3.500A) Proline residue: A1127 - end of helix Processing helix chain 'A' and resid 1139 through 1145 Processing helix chain 'A' and resid 1148 through 1201 Proline residue: A1168 - end of helix Processing helix chain 'A' and resid 1206 through 1248 removed outlier: 4.263A pdb=" N GLN A1218 " --> pdb=" O SER A1214 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ILE A1219 " --> pdb=" O TYR A1215 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N THR A1220 " --> pdb=" O ALA A1216 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N GLN A1221 " --> pdb=" O LEU A1217 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR A1222 " --> pdb=" O GLN A1218 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN A1224 " --> pdb=" O THR A1220 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL A1238 " --> pdb=" O GLU A1234 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N SER A1239 " --> pdb=" O THR A1235 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL A1240 " --> pdb=" O ASN A1236 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP A1248 " --> pdb=" O LYS A1244 " (cutoff:3.500A) Processing helix chain 'A' and resid 1312 through 1319 removed outlier: 4.324A pdb=" N THR A1316 " --> pdb=" O LYS A1312 " (cutoff:3.500A) Processing helix chain 'A' and resid 1337 through 1340 No H-bonds generated for 'chain 'A' and resid 1337 through 1340' Processing helix chain 'A' and resid 1343 through 1347 Processing helix chain 'A' and resid 1363 through 1367 Processing helix chain 'A' and resid 1376 through 1385 Processing helix chain 'A' and resid 1388 through 1393 Processing helix chain 'A' and resid 1405 through 1407 No H-bonds generated for 'chain 'A' and resid 1405 through 1407' Processing helix chain 'A' and resid 1412 through 1425 Processing helix chain 'A' and resid 1443 through 1454 Processing helix chain 'A' and resid 1468 through 1472 Processing sheet with id= A, first strand: chain 'A' and resid 613 through 615 removed outlier: 6.490A pdb=" N ALA A 625 " --> pdb=" O HIS A 690 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ALA A 653 " --> pdb=" O ALA A 625 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 831 through 835 removed outlier: 6.737A pdb=" N LEU A 825 " --> pdb=" O THR A 832 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLN A 834 " --> pdb=" O ILE A 823 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ILE A 823 " --> pdb=" O GLN A 834 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LYS A 807 " --> pdb=" O THR A 659 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ILE A 661 " --> pdb=" O LYS A 807 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU A 809 " --> pdb=" O ILE A 661 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1293 through 1296 Processing sheet with id= D, first strand: chain 'A' and resid 1476 through 1479 removed outlier: 3.693A pdb=" N ARG A1476 " --> pdb=" O LYS A1301 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY A1303 " --> pdb=" O ARG A1476 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE A1461 " --> pdb=" O VAL A1302 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ILE A1304 " --> pdb=" O ILE A1461 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N THR A1463 " --> pdb=" O ILE A1304 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N LEU A1431 " --> pdb=" O LEU A1462 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N ILE A1464 " --> pdb=" O LEU A1431 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU A1433 " --> pdb=" O ILE A1464 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 633 through 635 removed outlier: 6.302A pdb=" N LEU A 635 " --> pdb=" O ARG A 682 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ARG A 682 " --> pdb=" O LEU A 635 " (cutoff:3.500A) 649 hydrogen bonds defined for protein. 1848 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: 8.50 Time building geometry restraints manager: 18.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 10883 1.04 - 1.23: 412 1.23 - 1.43: 4244 1.43 - 1.63: 6382 1.63 - 1.83: 77 Bond restraints: 21998 Sorted by residual: bond pdb=" OG1 TPO A 911 " pdb=" P TPO A 911 " ideal model delta sigma weight residual 1.717 1.611 0.106 2.00e-02 2.50e+03 2.81e+01 bond pdb=" O1P TPO A 911 " pdb=" P TPO A 911 " ideal model delta sigma weight residual 1.525 1.611 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" O2P TPO A 911 " pdb=" P TPO A 911 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" N ILE A 792 " pdb=" CA ILE A 792 " ideal model delta sigma weight residual 1.461 1.499 -0.038 1.17e-02 7.31e+03 1.04e+01 bond pdb=" N CYS A1017 " pdb=" CA CYS A1017 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.19e-02 7.06e+03 9.72e+00 ... (remaining 21993 not shown) Histogram of bond angle deviations from ideal: 99.98 - 106.92: 909 106.92 - 113.86: 25646 113.86 - 120.80: 8227 120.80 - 127.74: 4873 127.74 - 134.68: 104 Bond angle restraints: 39759 Sorted by residual: angle pdb=" N HIS A 790 " pdb=" CA HIS A 790 " pdb=" C HIS A 790 " ideal model delta sigma weight residual 111.28 105.90 5.38 1.09e+00 8.42e-01 2.44e+01 angle pdb=" N ASN A 799 " pdb=" CA ASN A 799 " pdb=" C ASN A 799 " ideal model delta sigma weight residual 112.26 106.12 6.14 1.32e+00 5.74e-01 2.16e+01 angle pdb=" N PRO A 798 " pdb=" CA PRO A 798 " pdb=" C PRO A 798 " ideal model delta sigma weight residual 113.53 107.42 6.11 1.39e+00 5.18e-01 1.93e+01 angle pdb=" CA THR A1018 " pdb=" C THR A1018 " pdb=" O THR A1018 " ideal model delta sigma weight residual 121.00 116.49 4.51 1.05e+00 9.07e-01 1.84e+01 angle pdb=" CA HIS A 794 " pdb=" C HIS A 794 " pdb=" O HIS A 794 " ideal model delta sigma weight residual 120.55 116.17 4.38 1.06e+00 8.90e-01 1.71e+01 ... (remaining 39754 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 9309 17.91 - 35.82: 747 35.82 - 53.73: 184 53.73 - 71.64: 71 71.64 - 89.55: 11 Dihedral angle restraints: 10322 sinusoidal: 5514 harmonic: 4808 Sorted by residual: dihedral pdb=" CB CYS A 946 " pdb=" SG CYS A 946 " pdb=" SG CYS A1017 " pdb=" CB CYS A1017 " ideal model delta sinusoidal sigma weight residual 93.00 147.92 -54.92 1 1.00e+01 1.00e-02 4.08e+01 dihedral pdb=" CA TRP A 636 " pdb=" C TRP A 636 " pdb=" N GLN A 637 " pdb=" CA GLN A 637 " ideal model delta harmonic sigma weight residual -180.00 -155.39 -24.61 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA THR A 603 " pdb=" C THR A 603 " pdb=" N ASN A 604 " pdb=" CA ASN A 604 " ideal model delta harmonic sigma weight residual 180.00 156.24 23.76 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 10319 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1251 0.038 - 0.076: 352 0.076 - 0.114: 119 0.114 - 0.151: 41 0.151 - 0.189: 11 Chirality restraints: 1774 Sorted by residual: chirality pdb=" CB VAL A 618 " pdb=" CA VAL A 618 " pdb=" CG1 VAL A 618 " pdb=" CG2 VAL A 618 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.95e-01 chirality pdb=" CA THR A1018 " pdb=" N THR A1018 " pdb=" C THR A1018 " pdb=" CB THR A1018 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 8.71e-01 chirality pdb=" CA VAL A 699 " pdb=" N VAL A 699 " pdb=" C VAL A 699 " pdb=" CB VAL A 699 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.31e-01 ... (remaining 1771 not shown) Planarity restraints: 3220 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 802 " 0.016 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C LEU A 802 " -0.056 2.00e-02 2.50e+03 pdb=" O LEU A 802 " 0.020 2.00e-02 2.50e+03 pdb=" N HIS A 803 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 632 " -0.015 2.00e-02 2.50e+03 2.99e-02 8.95e+00 pdb=" C ALA A 632 " 0.052 2.00e-02 2.50e+03 pdb=" O ALA A 632 " -0.020 2.00e-02 2.50e+03 pdb=" N THR A 633 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 646 " -0.014 2.00e-02 2.50e+03 2.92e-02 8.54e+00 pdb=" C LEU A 646 " 0.051 2.00e-02 2.50e+03 pdb=" O LEU A 646 " -0.019 2.00e-02 2.50e+03 pdb=" N LYS A 647 " -0.017 2.00e-02 2.50e+03 ... (remaining 3217 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.32: 4605 2.32 - 2.89: 48814 2.89 - 3.46: 55014 3.46 - 4.03: 69810 4.03 - 4.60: 107278 Nonbonded interactions: 285521 Sorted by model distance: nonbonded pdb=" H GLY A 622 " pdb=" O LYS A 655 " model vdw 1.747 1.850 nonbonded pdb=" HH TYR A1110 " pdb=" OD1 ASN A1173 " model vdw 1.765 1.850 nonbonded pdb=" O ALA A 396 " pdb=" HG SER A 400 " model vdw 1.783 1.850 nonbonded pdb=" O VAL A 543 " pdb=" HG1 THR A 547 " model vdw 1.783 1.850 nonbonded pdb=" O GLY A 705 " pdb=" H VAL A 746 " model vdw 1.785 1.850 ... (remaining 285516 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.58 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: 1.570 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: 0.300 Extract box with map and model: 6.850 Check model and map are aligned: 0.340 Set scattering table: 0.190 Process input model: 69.820 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 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 : 0.006 0.106 11100 Z= 0.367 Angle : 0.867 10.075 15064 Z= 0.482 Chirality : 0.044 0.189 1774 Planarity : 0.005 0.050 1876 Dihedral : 13.253 89.553 3979 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 0.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.29 % Allowed : 7.97 % Favored : 90.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.21), residues: 1371 helix: 0.87 (0.16), residues: 909 sheet: -0.56 (0.51), residues: 76 loop : -2.15 (0.28), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 225 HIS 0.010 0.001 HIS A 803 PHE 0.016 0.002 PHE A 634 TYR 0.038 0.002 TYR A 991 ARG 0.005 0.001 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 40 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue MET 76 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue TYR 107 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue VAL 116 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue TYR 164 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue ILE 200 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LYS 517 is missing expected H atoms. Skipping. Residue LEU 522 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LYS 654 is missing expected H atoms. Skipping. Residue LYS 655 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue SER 980 is missing expected H atoms. Skipping. Residue TYR 1281 is missing expected H atoms. Skipping. Residue ILE 1304 is missing expected H atoms. Skipping. Residue SER 1395 is missing expected H atoms. Skipping. Residue LEU 1417 is missing expected H atoms. Skipping. Residue LYS 1457 is missing expected H atoms. Skipping. Evaluate side-chains 415 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 400 time to evaluate : 1.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 ASN cc_start: 0.8305 (m110) cc_final: 0.7895 (m110) REVERT: A 176 GLN cc_start: 0.8622 (tt0) cc_final: 0.8343 (tt0) REVERT: A 226 MET cc_start: 0.8326 (mmm) cc_final: 0.7657 (mmm) REVERT: A 467 ARG cc_start: 0.8213 (tpt170) cc_final: 0.7410 (mtp180) REVERT: A 485 ARG cc_start: 0.8289 (ttp80) cc_final: 0.7411 (mmp80) REVERT: A 486 VAL cc_start: 0.8746 (t) cc_final: 0.8206 (p) REVERT: A 504 LYS cc_start: 0.8687 (ttpp) cc_final: 0.8276 (tptt) REVERT: A 718 ASP cc_start: 0.7909 (t0) cc_final: 0.7421 (m-30) REVERT: A 735 LEU cc_start: 0.8350 (mp) cc_final: 0.8064 (tp) REVERT: A 789 ARG cc_start: 0.8744 (ttt180) cc_final: 0.8268 (ttp80) REVERT: A 962 MET cc_start: 0.8787 (tpp) cc_final: 0.8364 (tpp) REVERT: A 966 VAL cc_start: 0.9529 (t) cc_final: 0.9322 (m) REVERT: A 1029 MET cc_start: 0.8704 (tpt) cc_final: 0.8414 (tpp) REVERT: A 1048 ARG cc_start: 0.7803 (ttt180) cc_final: 0.7308 (ttm110) REVERT: A 1107 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.8515 (tm-30) REVERT: A 1108 GLN cc_start: 0.8389 (tp40) cc_final: 0.8062 (tp-100) REVERT: A 1319 LEU cc_start: 0.8751 (tp) cc_final: 0.8499 (tp) REVERT: A 1386 HIS cc_start: 0.7332 (t-90) cc_final: 0.6936 (m-70) REVERT: A 1390 HIS cc_start: 0.7108 (t70) cc_final: 0.6424 (t70) REVERT: A 1394 MET cc_start: 0.4952 (mtt) cc_final: 0.4655 (mpp) REVERT: A 1482 ASN cc_start: 0.6964 (m110) cc_final: 0.6551 (t0) outliers start: 15 outliers final: 2 residues processed: 411 average time/residue: 0.5212 time to fit residues: 303.9136 Evaluate side-chains 284 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 281 time to evaluate : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 1107 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 117 optimal weight: 8.9990 chunk 105 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 71 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 126 optimal weight: 30.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 ASN A 969 ASN A1027 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 11100 Z= 0.301 Angle : 0.611 7.031 15064 Z= 0.337 Chirality : 0.038 0.164 1774 Planarity : 0.004 0.042 1876 Dihedral : 6.042 80.047 1504 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.83 % Allowed : 16.28 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.22), residues: 1371 helix: 1.52 (0.17), residues: 901 sheet: -0.75 (0.52), residues: 76 loop : -1.96 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 422 HIS 0.011 0.001 HIS A 803 PHE 0.021 0.002 PHE A 634 TYR 0.014 0.002 TYR A 506 ARG 0.002 0.000 ARG A 990 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 40 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue MET 76 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue TYR 107 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue VAL 116 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue TYR 164 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue ILE 200 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LYS 517 is missing expected H atoms. Skipping. Residue LEU 522 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LYS 654 is missing expected H atoms. Skipping. Residue LYS 655 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue SER 980 is missing expected H atoms. Skipping. Residue TYR 1281 is missing expected H atoms. Skipping. Residue ILE 1304 is missing expected H atoms. Skipping. Residue SER 1395 is missing expected H atoms. Skipping. Residue LEU 1417 is missing expected H atoms. Skipping. Residue LYS 1457 is missing expected H atoms. Skipping. Evaluate side-chains 307 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 274 time to evaluate : 1.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.6505 (p0) cc_final: 0.6302 (p0) REVERT: A 56 LEU cc_start: 0.8258 (tp) cc_final: 0.8035 (tp) REVERT: A 410 SER cc_start: 0.9095 (t) cc_final: 0.8567 (p) REVERT: A 467 ARG cc_start: 0.8231 (tpt170) cc_final: 0.7373 (mtp180) REVERT: A 485 ARG cc_start: 0.8366 (ttp80) cc_final: 0.7619 (mmp80) REVERT: A 504 LYS cc_start: 0.8912 (ttpp) cc_final: 0.8542 (tptp) REVERT: A 718 ASP cc_start: 0.7865 (t0) cc_final: 0.7305 (m-30) REVERT: A 735 LEU cc_start: 0.8416 (mp) cc_final: 0.8154 (tp) REVERT: A 789 ARG cc_start: 0.8727 (ttt180) cc_final: 0.8303 (tmt-80) REVERT: A 813 LYS cc_start: 0.8815 (tptm) cc_final: 0.8476 (tppt) REVERT: A 962 MET cc_start: 0.8755 (tpp) cc_final: 0.8514 (tpp) REVERT: A 1029 MET cc_start: 0.8783 (tpt) cc_final: 0.8458 (tpp) REVERT: A 1048 ARG cc_start: 0.8169 (ttt180) cc_final: 0.7652 (ttm110) REVERT: A 1107 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.8561 (tm-30) REVERT: A 1110 TYR cc_start: 0.8811 (t80) cc_final: 0.8540 (t80) REVERT: A 1292 ILE cc_start: 0.8009 (pt) cc_final: 0.7595 (mp) REVERT: A 1390 HIS cc_start: 0.7181 (t70) cc_final: 0.6698 (t70) REVERT: A 1394 MET cc_start: 0.5102 (mtt) cc_final: 0.4782 (mpp) REVERT: A 1458 ASP cc_start: 0.8353 (m-30) cc_final: 0.8146 (t0) REVERT: A 1473 ASP cc_start: 0.8058 (t70) cc_final: 0.7557 (m-30) REVERT: A 1482 ASN cc_start: 0.7078 (m110) cc_final: 0.6621 (t0) outliers start: 33 outliers final: 23 residues processed: 292 average time/residue: 0.4598 time to fit residues: 193.9774 Evaluate side-chains 275 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 251 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 978 VAL Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1107 GLN Chi-restraints excluded: chain A residue 1126 SER Chi-restraints excluded: chain A residue 1231 VAL Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1349 LEU Chi-restraints excluded: chain A residue 1420 LEU Chi-restraints excluded: chain A residue 1452 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 70 optimal weight: 7.9990 chunk 39 optimal weight: 8.9990 chunk 105 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 126 optimal weight: 7.9990 chunk 136 optimal weight: 9.9990 chunk 112 optimal weight: 7.9990 chunk 125 optimal weight: 9.9990 chunk 43 optimal weight: 9.9990 chunk 101 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 GLN A1027 ASN A1466 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11100 Z= 0.321 Angle : 0.619 8.309 15064 Z= 0.341 Chirality : 0.038 0.170 1774 Planarity : 0.004 0.044 1876 Dihedral : 6.039 77.054 1500 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.26 % Allowed : 18.51 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.22), residues: 1371 helix: 1.29 (0.17), residues: 893 sheet: -0.92 (0.54), residues: 74 loop : -1.97 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 225 HIS 0.010 0.001 HIS A 803 PHE 0.022 0.002 PHE A 115 TYR 0.016 0.002 TYR A1105 ARG 0.010 0.001 ARG A 309 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 40 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue MET 76 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue TYR 107 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue VAL 116 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue TYR 164 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue ILE 200 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LYS 517 is missing expected H atoms. Skipping. Residue LEU 522 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LYS 654 is missing expected H atoms. Skipping. Residue LYS 655 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue SER 980 is missing expected H atoms. Skipping. Residue TYR 1281 is missing expected H atoms. Skipping. Residue ILE 1304 is missing expected H atoms. Skipping. Residue SER 1395 is missing expected H atoms. Skipping. Residue LEU 1417 is missing expected H atoms. Skipping. Residue LYS 1457 is missing expected H atoms. Skipping. Evaluate side-chains 281 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 243 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.6558 (p0) cc_final: 0.6178 (p0) REVERT: A 467 ARG cc_start: 0.8355 (tpt170) cc_final: 0.7388 (mtm180) REVERT: A 485 ARG cc_start: 0.8460 (ttp80) cc_final: 0.7596 (mmp80) REVERT: A 504 LYS cc_start: 0.9023 (ttpp) cc_final: 0.8654 (tptt) REVERT: A 525 LEU cc_start: 0.9023 (mp) cc_final: 0.8737 (mp) REVERT: A 718 ASP cc_start: 0.7986 (t0) cc_final: 0.7267 (m-30) REVERT: A 735 LEU cc_start: 0.8503 (mp) cc_final: 0.8229 (tp) REVERT: A 789 ARG cc_start: 0.8720 (ttt180) cc_final: 0.8268 (tmt-80) REVERT: A 813 LYS cc_start: 0.8715 (tptm) cc_final: 0.8323 (tppt) REVERT: A 1048 ARG cc_start: 0.8205 (ttt180) cc_final: 0.7589 (ttm110) REVERT: A 1110 TYR cc_start: 0.8799 (t80) cc_final: 0.8470 (t80) REVERT: A 1292 ILE cc_start: 0.8375 (pt) cc_final: 0.7998 (mp) REVERT: A 1390 HIS cc_start: 0.7281 (t70) cc_final: 0.7075 (t-90) REVERT: A 1472 MET cc_start: 0.5128 (mmt) cc_final: 0.4886 (mmt) REVERT: A 1482 ASN cc_start: 0.6980 (m110) cc_final: 0.6586 (t0) outliers start: 38 outliers final: 31 residues processed: 263 average time/residue: 0.5003 time to fit residues: 191.3698 Evaluate side-chains 265 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 234 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1061 ASP Chi-restraints excluded: chain A residue 1083 THR Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1213 LEU Chi-restraints excluded: chain A residue 1231 VAL Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1349 LEU Chi-restraints excluded: chain A residue 1420 LEU Chi-restraints excluded: chain A residue 1444 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 124 optimal weight: 20.0000 chunk 95 optimal weight: 8.9990 chunk 65 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 60 optimal weight: 7.9990 chunk 84 optimal weight: 30.0000 chunk 126 optimal weight: 30.0000 chunk 134 optimal weight: 30.0000 chunk 66 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 GLN A 272 ASN A 613 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.4850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 11100 Z= 0.427 Angle : 0.669 6.318 15064 Z= 0.378 Chirality : 0.040 0.166 1774 Planarity : 0.005 0.053 1876 Dihedral : 5.992 72.701 1497 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 4.63 % Allowed : 18.85 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.22), residues: 1371 helix: 0.66 (0.16), residues: 901 sheet: -1.17 (0.53), residues: 74 loop : -2.18 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 225 HIS 0.011 0.002 HIS A 803 PHE 0.030 0.002 PHE A 996 TYR 0.020 0.002 TYR A1105 ARG 0.004 0.000 ARG A1179 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 40 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue MET 76 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue TYR 107 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue VAL 116 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue TYR 164 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue ILE 200 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LYS 517 is missing expected H atoms. Skipping. Residue LEU 522 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LYS 654 is missing expected H atoms. Skipping. Residue LYS 655 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue SER 980 is missing expected H atoms. Skipping. Residue TYR 1281 is missing expected H atoms. Skipping. Residue ILE 1304 is missing expected H atoms. Skipping. Residue SER 1395 is missing expected H atoms. Skipping. Residue LEU 1417 is missing expected H atoms. Skipping. Residue LYS 1457 is missing expected H atoms. Skipping. Evaluate side-chains 277 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 223 time to evaluate : 1.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.6401 (p0) cc_final: 0.6132 (p0) REVERT: A 67 ARG cc_start: 0.6022 (mmt-90) cc_final: 0.5817 (mmp80) REVERT: A 146 ASN cc_start: 0.8408 (m110) cc_final: 0.7924 (m110) REVERT: A 343 VAL cc_start: 0.9314 (m) cc_final: 0.9106 (p) REVERT: A 466 MET cc_start: 0.7658 (ppp) cc_final: 0.7414 (ppp) REVERT: A 467 ARG cc_start: 0.8466 (tpt170) cc_final: 0.7463 (mtm180) REVERT: A 485 ARG cc_start: 0.8349 (ttp80) cc_final: 0.7651 (mmp80) REVERT: A 504 LYS cc_start: 0.9125 (ttpp) cc_final: 0.8792 (tptt) REVERT: A 735 LEU cc_start: 0.8335 (mp) cc_final: 0.8075 (tp) REVERT: A 789 ARG cc_start: 0.8769 (ttt180) cc_final: 0.8227 (tmt-80) REVERT: A 962 MET cc_start: 0.8816 (tpp) cc_final: 0.8579 (tpp) REVERT: A 1048 ARG cc_start: 0.8179 (ttt180) cc_final: 0.7630 (ttm110) REVERT: A 1110 TYR cc_start: 0.8793 (t80) cc_final: 0.8388 (t80) REVERT: A 1292 ILE cc_start: 0.8455 (pt) cc_final: 0.8092 (mp) REVERT: A 1482 ASN cc_start: 0.6999 (m110) cc_final: 0.6611 (t0) outliers start: 54 outliers final: 45 residues processed: 250 average time/residue: 0.4597 time to fit residues: 167.3530 Evaluate side-chains 262 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 217 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1018 THR Chi-restraints excluded: chain A residue 1061 ASP Chi-restraints excluded: chain A residue 1083 THR Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1107 GLN Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1126 SER Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1196 VAL Chi-restraints excluded: chain A residue 1231 VAL Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1274 PHE Chi-restraints excluded: chain A residue 1349 LEU Chi-restraints excluded: chain A residue 1420 LEU Chi-restraints excluded: chain A residue 1444 THR Chi-restraints excluded: chain A residue 1452 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 111 optimal weight: 0.7980 chunk 76 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 100 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 120 optimal weight: 8.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.4792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11100 Z= 0.148 Angle : 0.529 5.952 15064 Z= 0.280 Chirality : 0.036 0.172 1774 Planarity : 0.003 0.040 1876 Dihedral : 5.442 68.150 1497 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.08 % Allowed : 19.71 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.23), residues: 1371 helix: 1.40 (0.17), residues: 901 sheet: -0.98 (0.55), residues: 68 loop : -1.76 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 422 HIS 0.007 0.001 HIS A1390 PHE 0.018 0.001 PHE A 115 TYR 0.012 0.001 TYR A1105 ARG 0.003 0.000 ARG A 682 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 40 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue MET 76 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue TYR 107 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue VAL 116 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue TYR 164 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue ILE 200 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LYS 517 is missing expected H atoms. Skipping. Residue LEU 522 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LYS 654 is missing expected H atoms. Skipping. Residue LYS 655 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue SER 980 is missing expected H atoms. Skipping. Residue TYR 1281 is missing expected H atoms. Skipping. Residue ILE 1304 is missing expected H atoms. Skipping. Residue SER 1395 is missing expected H atoms. Skipping. Residue LEU 1417 is missing expected H atoms. Skipping. Residue LYS 1457 is missing expected H atoms. Skipping. Evaluate side-chains 278 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 242 time to evaluate : 1.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.6622 (p0) cc_final: 0.6245 (p0) REVERT: A 67 ARG cc_start: 0.6122 (mmt-90) cc_final: 0.5882 (mmp80) REVERT: A 343 VAL cc_start: 0.9264 (m) cc_final: 0.9034 (p) REVERT: A 466 MET cc_start: 0.7596 (ppp) cc_final: 0.7373 (ppp) REVERT: A 467 ARG cc_start: 0.8395 (tpt170) cc_final: 0.7375 (mtm180) REVERT: A 485 ARG cc_start: 0.8373 (ttp80) cc_final: 0.7609 (mmp80) REVERT: A 504 LYS cc_start: 0.9053 (ttpp) cc_final: 0.8685 (tptt) REVERT: A 718 ASP cc_start: 0.8000 (t0) cc_final: 0.7249 (m-30) REVERT: A 735 LEU cc_start: 0.8219 (mp) cc_final: 0.7937 (tp) REVERT: A 789 ARG cc_start: 0.8673 (ttt180) cc_final: 0.8202 (tmt-80) REVERT: A 813 LYS cc_start: 0.8665 (tptm) cc_final: 0.8279 (tppt) REVERT: A 971 TRP cc_start: 0.6795 (m-10) cc_final: 0.6383 (m-10) REVERT: A 1029 MET cc_start: 0.8457 (tpp) cc_final: 0.8241 (tpp) REVERT: A 1048 ARG cc_start: 0.8192 (ttt180) cc_final: 0.7650 (ttm110) REVERT: A 1110 TYR cc_start: 0.8570 (t80) cc_final: 0.8252 (t80) REVERT: A 1292 ILE cc_start: 0.8363 (pt) cc_final: 0.7997 (mp) REVERT: A 1472 MET cc_start: 0.5059 (mmt) cc_final: 0.4820 (mmt) REVERT: A 1482 ASN cc_start: 0.6967 (m110) cc_final: 0.6591 (t0) outliers start: 36 outliers final: 31 residues processed: 256 average time/residue: 0.4621 time to fit residues: 172.5797 Evaluate side-chains 262 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 231 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1061 ASP Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1126 SER Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1213 LEU Chi-restraints excluded: chain A residue 1231 VAL Chi-restraints excluded: chain A residue 1274 PHE Chi-restraints excluded: chain A residue 1420 LEU Chi-restraints excluded: chain A residue 1452 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 45 optimal weight: 1.9990 chunk 120 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 78 optimal weight: 20.0000 chunk 33 optimal weight: 2.9990 chunk 134 optimal weight: 30.0000 chunk 111 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 chunk 70 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.5092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11100 Z= 0.261 Angle : 0.564 5.912 15064 Z= 0.308 Chirality : 0.037 0.162 1774 Planarity : 0.004 0.043 1876 Dihedral : 5.524 68.334 1497 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 3.17 % Allowed : 20.74 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.23), residues: 1371 helix: 1.32 (0.17), residues: 901 sheet: -0.98 (0.56), residues: 68 loop : -1.88 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1014 HIS 0.007 0.001 HIS A 803 PHE 0.020 0.001 PHE A1320 TYR 0.018 0.002 TYR A1105 ARG 0.004 0.000 ARG A1179 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 40 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue MET 76 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue TYR 107 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue VAL 116 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue TYR 164 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue ILE 200 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LYS 517 is missing expected H atoms. Skipping. Residue LEU 522 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LYS 654 is missing expected H atoms. Skipping. Residue LYS 655 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue SER 980 is missing expected H atoms. Skipping. Residue TYR 1281 is missing expected H atoms. Skipping. Residue ILE 1304 is missing expected H atoms. Skipping. Residue SER 1395 is missing expected H atoms. Skipping. Residue LEU 1417 is missing expected H atoms. Skipping. Residue LYS 1457 is missing expected H atoms. Skipping. Evaluate side-chains 261 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 224 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.6504 (p0) cc_final: 0.6267 (p0) REVERT: A 67 ARG cc_start: 0.6130 (mmt-90) cc_final: 0.5884 (mmp80) REVERT: A 442 LYS cc_start: 0.8629 (mmmt) cc_final: 0.8221 (tttt) REVERT: A 466 MET cc_start: 0.7583 (ppp) cc_final: 0.7320 (ppp) REVERT: A 467 ARG cc_start: 0.8442 (tpt170) cc_final: 0.7386 (mtm180) REVERT: A 485 ARG cc_start: 0.8370 (ttp80) cc_final: 0.7624 (mmp80) REVERT: A 504 LYS cc_start: 0.9104 (ttpp) cc_final: 0.8747 (tptt) REVERT: A 735 LEU cc_start: 0.8266 (mp) cc_final: 0.7991 (tp) REVERT: A 789 ARG cc_start: 0.8708 (ttt180) cc_final: 0.8175 (tmt-80) REVERT: A 971 TRP cc_start: 0.6945 (m-10) cc_final: 0.6518 (m-10) REVERT: A 1029 MET cc_start: 0.8455 (tpp) cc_final: 0.8225 (tpp) REVERT: A 1048 ARG cc_start: 0.8174 (ttt180) cc_final: 0.7703 (ttm110) REVERT: A 1110 TYR cc_start: 0.8748 (t80) cc_final: 0.8298 (t80) REVERT: A 1292 ILE cc_start: 0.8370 (pt) cc_final: 0.8012 (mp) REVERT: A 1472 MET cc_start: 0.5092 (mmt) cc_final: 0.4833 (mmt) REVERT: A 1482 ASN cc_start: 0.6961 (m110) cc_final: 0.6569 (t0) outliers start: 37 outliers final: 33 residues processed: 239 average time/residue: 0.4615 time to fit residues: 161.2822 Evaluate side-chains 258 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 225 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1061 ASP Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1126 SER Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1212 SER Chi-restraints excluded: chain A residue 1231 VAL Chi-restraints excluded: chain A residue 1274 PHE Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1349 LEU Chi-restraints excluded: chain A residue 1420 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 129 optimal weight: 7.9990 chunk 15 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 133 optimal weight: 10.0000 chunk 83 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.5237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11100 Z= 0.230 Angle : 0.546 5.867 15064 Z= 0.297 Chirality : 0.037 0.179 1774 Planarity : 0.004 0.041 1876 Dihedral : 5.479 67.387 1497 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 3.43 % Allowed : 21.42 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.23), residues: 1371 helix: 1.38 (0.17), residues: 898 sheet: -0.90 (0.57), residues: 68 loop : -1.89 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 427 HIS 0.006 0.001 HIS A 803 PHE 0.018 0.001 PHE A1320 TYR 0.017 0.001 TYR A1105 ARG 0.004 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 40 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue MET 76 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue TYR 107 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue VAL 116 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue TYR 164 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue ILE 200 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LYS 517 is missing expected H atoms. Skipping. Residue LEU 522 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LYS 654 is missing expected H atoms. Skipping. Residue LYS 655 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue SER 980 is missing expected H atoms. Skipping. Residue TYR 1281 is missing expected H atoms. Skipping. Residue ILE 1304 is missing expected H atoms. Skipping. Residue SER 1395 is missing expected H atoms. Skipping. Residue LEU 1417 is missing expected H atoms. Skipping. Residue LYS 1457 is missing expected H atoms. Skipping. Evaluate side-chains 269 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 229 time to evaluate : 1.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.6464 (p0) cc_final: 0.6207 (p0) REVERT: A 67 ARG cc_start: 0.6136 (mmt-90) cc_final: 0.5904 (mmp80) REVERT: A 442 LYS cc_start: 0.8670 (mmmt) cc_final: 0.8245 (tttt) REVERT: A 466 MET cc_start: 0.7650 (ppp) cc_final: 0.7405 (ppp) REVERT: A 467 ARG cc_start: 0.8505 (tpt170) cc_final: 0.7439 (mtm180) REVERT: A 485 ARG cc_start: 0.8381 (ttp80) cc_final: 0.7639 (mmp80) REVERT: A 504 LYS cc_start: 0.9141 (ttpp) cc_final: 0.8818 (tptt) REVERT: A 735 LEU cc_start: 0.8269 (mp) cc_final: 0.8001 (tp) REVERT: A 789 ARG cc_start: 0.8686 (ttt180) cc_final: 0.8206 (tmt-80) REVERT: A 962 MET cc_start: 0.8876 (tpp) cc_final: 0.8591 (tpp) REVERT: A 971 TRP cc_start: 0.6913 (m-10) cc_final: 0.6483 (m-10) REVERT: A 1029 MET cc_start: 0.8443 (tpp) cc_final: 0.8217 (tpp) REVERT: A 1048 ARG cc_start: 0.8190 (ttt180) cc_final: 0.7764 (ttm110) REVERT: A 1110 TYR cc_start: 0.8668 (t80) cc_final: 0.8293 (t80) REVERT: A 1292 ILE cc_start: 0.8381 (pt) cc_final: 0.8028 (mp) REVERT: A 1472 MET cc_start: 0.5121 (mmt) cc_final: 0.4878 (mmt) REVERT: A 1482 ASN cc_start: 0.6992 (m110) cc_final: 0.6580 (t0) outliers start: 40 outliers final: 38 residues processed: 245 average time/residue: 0.4515 time to fit residues: 162.2390 Evaluate side-chains 258 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 220 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 676 MET Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 957 PHE Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1061 ASP Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1126 SER Chi-restraints excluded: chain A residue 1212 SER Chi-restraints excluded: chain A residue 1231 VAL Chi-restraints excluded: chain A residue 1274 PHE Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1320 PHE Chi-restraints excluded: chain A residue 1326 SER Chi-restraints excluded: chain A residue 1349 LEU Chi-restraints excluded: chain A residue 1420 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 53 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 91 optimal weight: 9.9990 chunk 66 optimal weight: 0.9980 chunk 12 optimal weight: 8.9990 chunk 105 optimal weight: 3.9990 chunk 121 optimal weight: 20.0000 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.5362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11100 Z= 0.201 Angle : 0.537 5.878 15064 Z= 0.290 Chirality : 0.036 0.169 1774 Planarity : 0.003 0.041 1876 Dihedral : 5.391 66.521 1497 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.68 % Allowed : 21.77 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.23), residues: 1371 helix: 1.49 (0.17), residues: 899 sheet: -0.93 (0.54), residues: 74 loop : -1.83 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 502 HIS 0.007 0.001 HIS A1390 PHE 0.021 0.001 PHE A1040 TYR 0.015 0.001 TYR A1105 ARG 0.004 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 40 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue MET 76 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue TYR 107 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue VAL 116 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue TYR 164 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue ILE 200 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LYS 517 is missing expected H atoms. Skipping. Residue LEU 522 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LYS 654 is missing expected H atoms. Skipping. Residue LYS 655 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue SER 980 is missing expected H atoms. Skipping. Residue TYR 1281 is missing expected H atoms. Skipping. Residue ILE 1304 is missing expected H atoms. Skipping. Residue SER 1395 is missing expected H atoms. Skipping. Residue LEU 1417 is missing expected H atoms. Skipping. Residue LYS 1457 is missing expected H atoms. Skipping. Evaluate side-chains 264 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 221 time to evaluate : 1.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.6535 (p0) cc_final: 0.6252 (p0) REVERT: A 67 ARG cc_start: 0.6075 (mmt-90) cc_final: 0.5846 (mmp80) REVERT: A 442 LYS cc_start: 0.8668 (mmmt) cc_final: 0.8239 (tttt) REVERT: A 485 ARG cc_start: 0.8379 (ttp80) cc_final: 0.7625 (mmp80) REVERT: A 504 LYS cc_start: 0.9141 (ttpp) cc_final: 0.8795 (tptt) REVERT: A 735 LEU cc_start: 0.8256 (mp) cc_final: 0.7979 (tp) REVERT: A 789 ARG cc_start: 0.8675 (ttt180) cc_final: 0.8248 (tmt-80) REVERT: A 971 TRP cc_start: 0.6908 (m-10) cc_final: 0.6489 (m-10) REVERT: A 1029 MET cc_start: 0.8476 (tpp) cc_final: 0.8257 (tpp) REVERT: A 1048 ARG cc_start: 0.8180 (ttt180) cc_final: 0.7716 (ttm110) REVERT: A 1110 TYR cc_start: 0.8676 (t80) cc_final: 0.8302 (t80) REVERT: A 1292 ILE cc_start: 0.8429 (pt) cc_final: 0.8049 (mp) REVERT: A 1472 MET cc_start: 0.5161 (mmt) cc_final: 0.4886 (mmt) REVERT: A 1482 ASN cc_start: 0.6989 (m110) cc_final: 0.6581 (t0) outliers start: 43 outliers final: 42 residues processed: 236 average time/residue: 0.4417 time to fit residues: 154.0303 Evaluate side-chains 263 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 221 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 506 TYR Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 676 MET Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1061 ASP Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1126 SER Chi-restraints excluded: chain A residue 1212 SER Chi-restraints excluded: chain A residue 1213 LEU Chi-restraints excluded: chain A residue 1231 VAL Chi-restraints excluded: chain A residue 1274 PHE Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1320 PHE Chi-restraints excluded: chain A residue 1326 SER Chi-restraints excluded: chain A residue 1349 LEU Chi-restraints excluded: chain A residue 1420 LEU Chi-restraints excluded: chain A residue 1431 LEU Chi-restraints excluded: chain A residue 1477 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 128 optimal weight: 7.9990 chunk 117 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 112 optimal weight: 7.9990 chunk 118 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.5585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11100 Z= 0.282 Angle : 0.581 6.074 15064 Z= 0.319 Chirality : 0.037 0.171 1774 Planarity : 0.004 0.043 1876 Dihedral : 5.547 67.057 1497 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 3.94 % Allowed : 22.11 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.23), residues: 1371 helix: 1.22 (0.17), residues: 904 sheet: -0.88 (0.55), residues: 73 loop : -1.98 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 427 HIS 0.007 0.001 HIS A 803 PHE 0.018 0.002 PHE A 541 TYR 0.020 0.002 TYR A1105 ARG 0.005 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 40 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue MET 76 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue TYR 107 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue VAL 116 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue TYR 164 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue ILE 200 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LYS 517 is missing expected H atoms. Skipping. Residue LEU 522 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LYS 654 is missing expected H atoms. Skipping. Residue LYS 655 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue SER 980 is missing expected H atoms. Skipping. Residue TYR 1281 is missing expected H atoms. Skipping. Residue ILE 1304 is missing expected H atoms. Skipping. Residue SER 1395 is missing expected H atoms. Skipping. Residue LEU 1417 is missing expected H atoms. Skipping. Residue LYS 1457 is missing expected H atoms. Skipping. Evaluate side-chains 264 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 218 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.6405 (p0) cc_final: 0.6092 (p0) REVERT: A 67 ARG cc_start: 0.6177 (mmt-90) cc_final: 0.5966 (mmp80) REVERT: A 442 LYS cc_start: 0.8727 (mmmt) cc_final: 0.8272 (tttt) REVERT: A 485 ARG cc_start: 0.8365 (ttp80) cc_final: 0.7626 (mmp80) REVERT: A 504 LYS cc_start: 0.9171 (ttpp) cc_final: 0.8862 (tptt) REVERT: A 789 ARG cc_start: 0.8715 (ttt180) cc_final: 0.8217 (tmt-80) REVERT: A 971 TRP cc_start: 0.6925 (m-10) cc_final: 0.6519 (m-10) REVERT: A 1029 MET cc_start: 0.8443 (tpp) cc_final: 0.8211 (tpp) REVERT: A 1048 ARG cc_start: 0.8168 (ttt180) cc_final: 0.7731 (ttm110) REVERT: A 1110 TYR cc_start: 0.8735 (t80) cc_final: 0.8291 (t80) REVERT: A 1292 ILE cc_start: 0.8406 (pt) cc_final: 0.8045 (mp) REVERT: A 1472 MET cc_start: 0.5089 (mmt) cc_final: 0.4825 (mmt) REVERT: A 1482 ASN cc_start: 0.6946 (m110) cc_final: 0.6550 (t0) outliers start: 46 outliers final: 43 residues processed: 238 average time/residue: 0.4454 time to fit residues: 155.8286 Evaluate side-chains 258 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 215 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 506 TYR Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 651 PHE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 676 MET Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1061 ASP Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1126 SER Chi-restraints excluded: chain A residue 1212 SER Chi-restraints excluded: chain A residue 1231 VAL Chi-restraints excluded: chain A residue 1274 PHE Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1320 PHE Chi-restraints excluded: chain A residue 1326 SER Chi-restraints excluded: chain A residue 1349 LEU Chi-restraints excluded: chain A residue 1420 LEU Chi-restraints excluded: chain A residue 1431 LEU Chi-restraints excluded: chain A residue 1477 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 80 optimal weight: 8.9990 chunk 62 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 138 optimal weight: 9.9990 chunk 127 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 85 optimal weight: 8.9990 chunk 67 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.5789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11100 Z= 0.282 Angle : 0.581 5.942 15064 Z= 0.319 Chirality : 0.038 0.267 1774 Planarity : 0.004 0.043 1876 Dihedral : 5.619 66.546 1497 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 3.86 % Allowed : 22.71 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.23), residues: 1371 helix: 1.13 (0.17), residues: 904 sheet: -0.85 (0.56), residues: 72 loop : -1.99 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 427 HIS 0.006 0.001 HIS A 803 PHE 0.016 0.002 PHE A 541 TYR 0.020 0.002 TYR A1105 ARG 0.004 0.000 ARG A 156 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 40 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue MET 76 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue TYR 107 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue VAL 116 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue TYR 164 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue ILE 200 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LYS 517 is missing expected H atoms. Skipping. Residue LEU 522 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LYS 654 is missing expected H atoms. Skipping. Residue LYS 655 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue SER 980 is missing expected H atoms. Skipping. Residue TYR 1281 is missing expected H atoms. Skipping. Residue ILE 1304 is missing expected H atoms. Skipping. Residue SER 1395 is missing expected H atoms. Skipping. Residue LEU 1417 is missing expected H atoms. Skipping. Residue LYS 1457 is missing expected H atoms. Skipping. Evaluate side-chains 262 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 217 time to evaluate : 1.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.6428 (p0) cc_final: 0.6114 (p0) REVERT: A 67 ARG cc_start: 0.6161 (mmt-90) cc_final: 0.5942 (mmp80) REVERT: A 442 LYS cc_start: 0.8763 (mmmt) cc_final: 0.8286 (tttt) REVERT: A 485 ARG cc_start: 0.8372 (ttp80) cc_final: 0.7629 (mmp80) REVERT: A 504 LYS cc_start: 0.9165 (ttpp) cc_final: 0.8863 (tptt) REVERT: A 789 ARG cc_start: 0.8648 (ttt180) cc_final: 0.8217 (tmt-80) REVERT: A 971 TRP cc_start: 0.6930 (m-10) cc_final: 0.6516 (m-10) REVERT: A 1029 MET cc_start: 0.8439 (tpp) cc_final: 0.8211 (tpp) REVERT: A 1048 ARG cc_start: 0.8163 (ttt180) cc_final: 0.7744 (ttm110) REVERT: A 1110 TYR cc_start: 0.8697 (t80) cc_final: 0.8322 (t80) REVERT: A 1292 ILE cc_start: 0.8444 (pt) cc_final: 0.8084 (mp) REVERT: A 1472 MET cc_start: 0.5092 (mmt) cc_final: 0.4835 (mmt) REVERT: A 1482 ASN cc_start: 0.6989 (m110) cc_final: 0.6523 (t0) outliers start: 45 outliers final: 43 residues processed: 236 average time/residue: 0.4307 time to fit residues: 150.3542 Evaluate side-chains 256 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 213 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 676 MET Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1061 ASP Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1126 SER Chi-restraints excluded: chain A residue 1212 SER Chi-restraints excluded: chain A residue 1231 VAL Chi-restraints excluded: chain A residue 1274 PHE Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1320 PHE Chi-restraints excluded: chain A residue 1326 SER Chi-restraints excluded: chain A residue 1349 LEU Chi-restraints excluded: chain A residue 1420 LEU Chi-restraints excluded: chain A residue 1431 LEU Chi-restraints excluded: chain A residue 1477 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 33 optimal weight: 3.9990 chunk 101 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 110 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 113 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.142479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.114456 restraints weight = 81044.781| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 4.48 r_work: 0.3618 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3631 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3631 r_free = 0.3631 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3631 r_free = 0.3631 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3631 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.5811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11100 Z= 0.226 Angle : 0.556 6.341 15064 Z= 0.301 Chirality : 0.037 0.196 1774 Planarity : 0.003 0.042 1876 Dihedral : 5.513 65.637 1497 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 3.68 % Allowed : 22.88 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.23), residues: 1371 helix: 1.28 (0.17), residues: 907 sheet: -0.74 (0.56), residues: 72 loop : -2.00 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 502 HIS 0.006 0.001 HIS A 803 PHE 0.014 0.001 PHE A 576 TYR 0.017 0.001 TYR A1105 ARG 0.004 0.000 ARG A 156 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5094.16 seconds wall clock time: 90 minutes 5.93 seconds (5405.93 seconds total)