Starting phenix.real_space_refine on Tue Dec 12 15:01:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m69_23691/12_2023/7m69_23691_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m69_23691/12_2023/7m69_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_23691/12_2023/7m69_23691.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m69_23691/12_2023/7m69_23691.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m69_23691/12_2023/7m69_23691_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m69_23691/12_2023/7m69_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-1.21rc1-5172/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: 10.18, per 1000 atoms: 0.47 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: 17.77 Conformation dependent library (CDL) restraints added in 2.7 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: 5.51 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: 9.02 Time building geometry restraints manager: 18.47 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: 9221 17.91 - 35.82: 725 35.82 - 53.73: 127 53.73 - 71.64: 25 71.64 - 89.55: 11 Dihedral angle restraints: 10109 sinusoidal: 5301 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 10106 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: 1.190 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: 0.340 Extract box with map and model: 7.220 Check model and map are aligned: 0.360 Set scattering table: 0.220 Process input model: 75.580 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.240 ------------------------------------------------------------------------------- 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 : 1.750 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 outliers start: 15 outliers final: 2 residues processed: 411 average time/residue: 0.5156 time to fit residues: 298.6082 Evaluate side-chains 275 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 273 time to evaluate : 1.696 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.5319 time to fit residues: 3.4544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 35 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 42 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 chunk 126 optimal weight: 0.0470 overall best weight: 3.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 969 ASN A1027 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11100 Z= 0.236 Angle : 0.585 6.801 15064 Z= 0.318 Chirality : 0.037 0.165 1774 Planarity : 0.004 0.042 1876 Dihedral : 5.254 61.847 1495 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.23 % Allowed : 17.14 % Favored : 80.63 % 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: 0.72 (0.22), residues: 1371 helix: 1.58 (0.17), residues: 903 sheet: -0.67 (0.51), residues: 76 loop : -1.94 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 422 HIS 0.010 0.001 HIS A 803 PHE 0.018 0.001 PHE A 541 TYR 0.011 0.001 TYR A1105 ARG 0.003 0.000 ARG A1143 *********************** 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 302 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 276 time to evaluate : 1.868 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 outliers start: 26 outliers final: 19 residues processed: 286 average time/residue: 0.4542 time to fit residues: 192.9603 Evaluate side-chains 258 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 239 time to evaluate : 1.953 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 19 outliers final: 1 residues processed: 19 average time/residue: 0.2943 time to fit residues: 12.0494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 70 optimal weight: 0.6980 chunk 39 optimal weight: 7.9990 chunk 105 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 126 optimal weight: 20.0000 chunk 136 optimal weight: 10.0000 chunk 112 optimal weight: 7.9990 chunk 125 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 ASN A 613 GLN A 790 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11100 Z= 0.256 Angle : 0.580 6.894 15064 Z= 0.315 Chirality : 0.037 0.172 1774 Planarity : 0.004 0.039 1876 Dihedral : 5.221 63.470 1495 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.46 % Allowed : 19.02 % Favored : 79.52 % 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: 0.76 (0.23), residues: 1371 helix: 1.60 (0.17), residues: 901 sheet: -0.69 (0.52), residues: 76 loop : -1.86 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 225 HIS 0.008 0.001 HIS A 803 PHE 0.018 0.001 PHE A 634 TYR 0.013 0.001 TYR A1105 ARG 0.011 0.000 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 261 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 244 time to evaluate : 1.800 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 outliers start: 17 outliers final: 11 residues processed: 252 average time/residue: 0.4430 time to fit residues: 166.6528 Evaluate side-chains 246 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 235 time to evaluate : 1.807 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 3 residues processed: 11 average time/residue: 0.3130 time to fit residues: 8.0135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 124 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 chunk 126 optimal weight: 20.0000 chunk 134 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 120 optimal weight: 8.9990 chunk 36 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1466 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11100 Z= 0.242 Angle : 0.567 7.927 15064 Z= 0.307 Chirality : 0.037 0.169 1774 Planarity : 0.004 0.035 1876 Dihedral : 5.210 64.262 1495 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.97 % Allowed : 19.54 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.22), residues: 1371 helix: 1.52 (0.17), residues: 903 sheet: -0.63 (0.51), residues: 76 loop : -1.88 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 225 HIS 0.008 0.001 HIS A 803 PHE 0.017 0.001 PHE A 115 TYR 0.014 0.001 TYR A1105 ARG 0.002 0.000 ARG A 682 *********************** 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 255 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 232 time to evaluate : 1.814 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 outliers start: 23 outliers final: 16 residues processed: 238 average time/residue: 0.4429 time to fit residues: 162.3337 Evaluate side-chains 243 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 227 time to evaluate : 1.847 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 2 residues processed: 16 average time/residue: 0.2563 time to fit residues: 9.8786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 111 optimal weight: 9.9990 chunk 76 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 114 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 GLN ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.4791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11100 Z= 0.296 Angle : 0.589 5.964 15064 Z= 0.325 Chirality : 0.038 0.184 1774 Planarity : 0.004 0.043 1876 Dihedral : 5.345 66.029 1495 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 1.29 % Allowed : 19.71 % Favored : 79.01 % 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: 0.41 (0.22), residues: 1371 helix: 1.32 (0.17), residues: 900 sheet: -0.83 (0.51), residues: 74 loop : -1.98 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1014 HIS 0.008 0.001 HIS A 803 PHE 0.030 0.002 PHE A 996 TYR 0.017 0.002 TYR A1105 ARG 0.002 0.000 ARG A 344 *********************** 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 245 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 230 time to evaluate : 1.788 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 outliers start: 15 outliers final: 9 residues processed: 240 average time/residue: 0.4280 time to fit residues: 154.3146 Evaluate side-chains 225 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 216 time to evaluate : 1.869 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 9 average time/residue: 0.3280 time to fit residues: 7.1575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 45 optimal weight: 8.9990 chunk 120 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 78 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 62 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.5046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11100 Z= 0.219 Angle : 0.562 7.940 15064 Z= 0.301 Chirality : 0.037 0.238 1774 Planarity : 0.004 0.043 1876 Dihedral : 5.235 65.650 1495 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 1.37 % Allowed : 20.57 % Favored : 78.06 % 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: 0.52 (0.23), residues: 1371 helix: 1.41 (0.17), residues: 901 sheet: -0.94 (0.53), residues: 68 loop : -1.92 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1014 HIS 0.006 0.001 HIS A 803 PHE 0.025 0.001 PHE A1456 TYR 0.015 0.001 TYR A1105 ARG 0.002 0.000 ARG A 485 *********************** 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 246 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 230 time to evaluate : 1.779 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 outliers start: 16 outliers final: 13 residues processed: 235 average time/residue: 0.4520 time to fit residues: 158.4301 Evaluate side-chains 229 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 216 time to evaluate : 1.827 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 2 residues processed: 13 average time/residue: 0.2465 time to fit residues: 8.1440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 129 optimal weight: 9.9990 chunk 15 optimal weight: 0.8980 chunk 76 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 chunk 75 optimal weight: 9.9990 chunk 133 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.5322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11100 Z= 0.282 Angle : 0.584 6.169 15064 Z= 0.321 Chirality : 0.038 0.178 1774 Planarity : 0.004 0.046 1876 Dihedral : 5.327 66.191 1495 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 1.03 % Allowed : 21.59 % Favored : 77.38 % 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: 0.36 (0.22), residues: 1371 helix: 1.27 (0.17), residues: 902 sheet: -0.93 (0.54), residues: 69 loop : -1.97 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1014 HIS 0.007 0.001 HIS A 803 PHE 0.024 0.002 PHE A1320 TYR 0.018 0.002 TYR A1105 ARG 0.003 0.000 ARG A 614 *********************** 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 236 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 224 time to evaluate : 1.812 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 outliers start: 12 outliers final: 12 residues processed: 228 average time/residue: 0.4333 time to fit residues: 150.8145 Evaluate side-chains 230 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 218 time to evaluate : 1.792 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 2 residues processed: 12 average time/residue: 0.2672 time to fit residues: 7.9750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 53 optimal weight: 0.6980 chunk 80 optimal weight: 10.0000 chunk 40 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.5412 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= 0.188 Angle : 0.540 5.855 15064 Z= 0.291 Chirality : 0.036 0.173 1774 Planarity : 0.003 0.042 1876 Dihedral : 5.167 64.777 1495 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 0.77 % Allowed : 22.37 % Favored : 76.86 % 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: 0.59 (0.23), residues: 1371 helix: 1.46 (0.17), residues: 908 sheet: -0.90 (0.54), residues: 69 loop : -1.91 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1175 HIS 0.005 0.001 HIS A 803 PHE 0.026 0.001 PHE A1320 TYR 0.014 0.001 TYR A1105 ARG 0.003 0.000 ARG A 614 *********************** 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 237 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 228 time to evaluate : 1.936 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 outliers start: 9 outliers final: 9 residues processed: 228 average time/residue: 0.4146 time to fit residues: 144.9075 Evaluate side-chains 228 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 219 time to evaluate : 1.779 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 9 average time/residue: 0.2494 time to fit residues: 6.2739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 128 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 chunk 124 optimal weight: 8.9990 chunk 75 optimal weight: 0.0470 chunk 54 optimal weight: 0.0270 chunk 98 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 118 optimal weight: 9.9990 chunk 81 optimal weight: 0.9990 chunk 132 optimal weight: 9.9990 overall best weight: 2.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.5434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11100 Z= 0.171 Angle : 0.533 5.994 15064 Z= 0.286 Chirality : 0.036 0.192 1774 Planarity : 0.003 0.041 1876 Dihedral : 5.036 63.581 1495 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.51 % Allowed : 23.31 % Favored : 76.18 % 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: 0.78 (0.23), residues: 1371 helix: 1.62 (0.17), residues: 908 sheet: -0.83 (0.55), residues: 69 loop : -1.89 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1175 HIS 0.005 0.001 HIS A 803 PHE 0.014 0.001 PHE A 634 TYR 0.013 0.001 TYR A1105 ARG 0.004 0.000 ARG A 682 *********************** 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 231 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 225 time to evaluate : 1.737 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 outliers start: 6 outliers final: 4 residues processed: 228 average time/residue: 0.4435 time to fit residues: 155.9324 Evaluate side-chains 224 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 220 time to evaluate : 1.811 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 4 average time/residue: 0.2993 time to fit residues: 4.6071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 80 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 138 optimal weight: 8.9990 chunk 127 optimal weight: 6.9990 chunk 110 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 87 optimal weight: 0.7980 chunk 117 optimal weight: 9.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.5563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11100 Z= 0.189 Angle : 0.548 6.570 15064 Z= 0.292 Chirality : 0.036 0.183 1774 Planarity : 0.003 0.042 1876 Dihedral : 5.028 66.050 1495 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.43 % Allowed : 23.65 % Favored : 75.92 % 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: 0.79 (0.23), residues: 1371 helix: 1.61 (0.17), residues: 907 sheet: -0.72 (0.54), residues: 71 loop : -1.88 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 849 HIS 0.005 0.001 HIS A 803 PHE 0.016 0.001 PHE A 954 TYR 0.018 0.001 TYR A 500 ARG 0.008 0.000 ARG A1415 ********************** 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 224 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 219 time to evaluate : 1.821 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 outliers start: 5 outliers final: 4 residues processed: 220 average time/residue: 0.4140 time to fit residues: 142.2659 Evaluate side-chains 222 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 218 time to evaluate : 1.843 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 4 average time/residue: 0.2544 time to fit residues: 4.1558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 113 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.146563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.119258 restraints weight = 80886.236| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 4.12 r_work: 0.3694 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3697 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3697 r_free = 0.3697 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3697 r_free = 0.3697 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3697 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.5610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11100 Z= 0.169 Angle : 0.535 6.438 15064 Z= 0.285 Chirality : 0.036 0.182 1774 Planarity : 0.003 0.041 1876 Dihedral : 4.945 67.824 1495 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.60 % Allowed : 23.56 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.23), residues: 1371 helix: 1.72 (0.17), residues: 907 sheet: -0.60 (0.54), residues: 71 loop : -1.87 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1175 HIS 0.005 0.001 HIS A 803 PHE 0.013 0.001 PHE A 115 TYR 0.018 0.001 TYR A 500 ARG 0.004 0.000 ARG A 206 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5295.26 seconds wall clock time: 94 minutes 22.32 seconds (5662.32 seconds total)