Starting phenix.real_space_refine on Sun Feb 18 10:39:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m68_23690/02_2024/7m68_23690_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m68_23690/02_2024/7m68_23690.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m68_23690/02_2024/7m68_23690.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m68_23690/02_2024/7m68_23690.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m68_23690/02_2024/7m68_23690_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m68_23690/02_2024/7m68_23690_trim_updated.pdb" } resolution = 4.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.907 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 46 5.16 5 C 7024 2.51 5 N 1833 2.21 5 O 1981 1.98 5 H 10919 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-5238/modules/chem_data/mon_lib" Total number of atoms: 21806 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 21806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1390, 21806 Classifications: {'peptide': 1390} Link IDs: {'PTRANS': 37, 'TRANS': 1352} Chain breaks: 4 Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 280 Unresolved non-hydrogen dihedrals: 191 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 4, 'TPO:plan-1': 1, 'ASP:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 129 Time building chain proxies: 10.06, per 1000 atoms: 0.46 Number of scatterers: 21806 At special positions: 0 Unit cell: (131.968, 117.534, 103.1, 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 46 16.00 P 3 15.00 O 1981 8.00 N 1833 7.00 C 7024 6.00 H 10919 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=2.05 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: 17.48 Conformation dependent library (CDL) restraints added in 2.1 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 6 sheets defined 64.6% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.58 Creating SS restraints... Processing helix chain 'A' and resid 30 through 60 removed outlier: 3.671A pdb=" N GLY A 49 " --> pdb=" O MET A 45 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LEU A 53 " --> pdb=" O GLY A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 91 Processing helix chain 'A' and resid 94 through 97 removed outlier: 3.627A pdb=" N GLU A 97 " --> pdb=" O SER A 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 94 through 97' Processing helix chain 'A' and resid 101 through 123 removed outlier: 4.332A pdb=" N LEU A 120 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE A 123 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 159 Processing helix chain 'A' and resid 168 through 188 removed outlier: 3.852A pdb=" N ILE A 171 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 174 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 183 " --> pdb=" O CYS A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 201 removed outlier: 3.716A 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 211 through 213 No H-bonds generated for 'chain 'A' and resid 211 through 213' Processing helix chain 'A' and resid 217 through 222 removed outlier: 3.642A pdb=" N THR A 222 " --> pdb=" O PHE A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 234 Processing helix chain 'A' and resid 252 through 268 removed outlier: 3.678A pdb=" N ASN A 262 " --> pdb=" O LYS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 327 removed outlier: 3.778A pdb=" N LEU A 275 " --> pdb=" O ASN A 272 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG A 281 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR A 282 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLY A 284 " --> pdb=" O ARG A 281 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N SER A 285 " --> pdb=" O THR A 282 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS A 286 " --> pdb=" O PHE A 283 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 299 " --> pdb=" O ILE A 296 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N PHE A 302 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN A 304 " --> pdb=" O ALA A 301 " (cutoff:3.500A) Proline residue: A 305 - end of helix removed outlier: 3.501A pdb=" N ILE A 310 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR A 316 " --> pdb=" O LYS A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 390 removed outlier: 3.735A pdb=" N ALA A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 398 Processing helix chain 'A' and resid 402 through 419 removed outlier: 4.358A pdb=" N VAL A 413 " --> pdb=" O MET A 409 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN A 414 " --> pdb=" O SER A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 443 removed outlier: 4.176A pdb=" N GLY A 429 " --> pdb=" O ILE A 426 " (cutoff:3.500A) Proline residue: A 430 - end of helix removed outlier: 3.569A pdb=" N ILE A 435 " --> pdb=" O GLN A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 492 Proline residue: A 460 - end of helix Processing helix chain 'A' and resid 494 through 500 Processing helix chain 'A' and resid 503 through 537 removed outlier: 3.713A pdb=" N ASN A 516 " --> pdb=" O GLU A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 554 removed outlier: 4.193A pdb=" N ALA A 549 " --> pdb=" O CYS A 545 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL A 552 " --> pdb=" O PHE A 548 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N TYR A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 603 removed outlier: 4.497A pdb=" N PHE A 576 " --> pdb=" O ASN A 572 " (cutoff:3.500A) Proline residue: A 577 - end of helix Proline residue: A 582 - end of helix removed outlier: 4.191A pdb=" N LEU A 585 " --> pdb=" O ILE A 581 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN A 586 " --> pdb=" O PRO A 582 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER A 587 " --> pdb=" O MET A 583 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER A 592 " --> pdb=" O PHE A 588 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL A 593 " --> pdb=" O ILE A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 676 Processing helix chain 'A' and resid 707 through 711 Processing helix chain 'A' and resid 719 through 728 Processing helix chain 'A' and resid 732 through 738 removed outlier: 4.291A 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 795 removed outlier: 3.504A pdb=" N HIS A 790 " --> pdb=" O HIS A 786 " (cutoff:3.500A) removed outlier: 3.807A 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 removed outlier: 3.512A pdb=" N LYS A 842 " --> pdb=" O ASP A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 849 No H-bonds generated for 'chain 'A' and resid 846 through 849' Processing helix chain 'A' and resid 918 through 929 removed outlier: 3.742A pdb=" N GLU A 921 " --> pdb=" O GLY A 918 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE A 923 " --> pdb=" O ASP A 920 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS A 925 " --> pdb=" O ASN A 922 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG A 929 " --> pdb=" O ARG A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 945 Processing helix chain 'A' and resid 948 through 981 Processing helix chain 'A' and resid 988 through 1034 removed outlier: 3.683A pdb=" N LEU A1013 " --> pdb=" O GLN A1009 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TRP A1014 " --> pdb=" O THR A1010 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ILE A1019 " --> pdb=" O VAL A1015 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N HIS A1020 " --> pdb=" O PHE A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1043 Processing helix chain 'A' and resid 1046 through 1088 removed outlier: 3.984A pdb=" N ILE A1057 " --> pdb=" O PHE A1053 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR A1058 " --> pdb=" O SER A1054 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU A1064 " --> pdb=" O VAL A1060 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLY A1065 " --> pdb=" O ASP A1061 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER A1069 " --> pdb=" O GLY A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1137 removed outlier: 4.169A pdb=" N ILE A1093 " --> pdb=" O TRP A1090 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N PHE A1094 " --> pdb=" O GLN A1091 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE A1097 " --> pdb=" O PHE A1094 " (cutoff:3.500A) Proline residue: A1098 - end of helix removed outlier: 4.732A pdb=" N ARG A1115 " --> pdb=" O ARG A1112 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG A1125 " --> pdb=" O SER A1122 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N SER A1126 " --> pdb=" O ILE A1123 " (cutoff:3.500A) Proline residue: A1127 - end of helix removed outlier: 3.637A pdb=" N THR A1135 " --> pdb=" O PHE A1132 " (cutoff:3.500A) 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 1247 removed outlier: 4.076A pdb=" N GLN A1218 " --> pdb=" O SER A1214 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ILE A1219 " --> pdb=" O TYR A1215 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N THR A1220 " --> pdb=" O ALA A1216 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N GLN A1221 " --> pdb=" O LEU A1217 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR A1222 " --> pdb=" O GLN A1218 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG A1228 " --> pdb=" O ASN A1224 " (cutoff:3.500A) Processing helix chain 'A' and resid 1312 through 1320 removed outlier: 3.912A pdb=" N THR A1316 " --> pdb=" O LYS A1312 " (cutoff:3.500A) Processing helix chain 'A' and resid 1337 through 1339 No H-bonds generated for 'chain 'A' and resid 1337 through 1339' Processing helix chain 'A' and resid 1343 through 1348 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 1412 through 1425 Processing helix chain 'A' and resid 1443 through 1454 Processing helix chain 'A' and resid 1468 through 1473 Processing sheet with id= A, first strand: chain 'A' and resid 613 through 615 removed outlier: 3.794A pdb=" N ILE A 626 " --> pdb=" O ALA A 653 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A 653 " --> pdb=" O ILE A 626 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 659 through 662 removed outlier: 6.578A pdb=" N SER A 822 " --> pdb=" O CYS A 660 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N VAL A 662 " --> pdb=" O SER A 822 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ALA A 824 " --> pdb=" O VAL A 662 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN A 833 " --> pdb=" O LEU A 825 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASP A 827 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ILE A 831 " --> pdb=" O ASP A 827 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 693 through 696 removed outlier: 6.422A pdb=" N THR A 773 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N VAL A 696 " --> pdb=" O THR A 773 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU A 775 " --> pdb=" O VAL A 696 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 1293 through 1296 Processing sheet with id= E, first strand: chain 'A' and resid 1476 through 1479 removed outlier: 3.525A pdb=" N GLY A1303 " --> pdb=" O ARG A1476 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU A1431 " --> pdb=" O LEU A1462 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ILE A1464 " --> pdb=" O LEU A1431 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU A1433 " --> pdb=" O ILE A1464 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 645 through 649 removed outlier: 5.480A pdb=" N ALA A 632 " --> pdb=" O ASN A 648 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU A 635 " --> pdb=" O ARG A 682 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ARG A 682 " --> pdb=" O LEU A 635 " (cutoff:3.500A) 651 hydrogen bonds defined for protein. 1575 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: 7.75 Time building geometry restraints manager: 18.05 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: 10904 1.04 - 1.25: 1570 1.25 - 1.45: 3231 1.45 - 1.66: 6242 1.66 - 1.87: 75 Bond restraints: 22022 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 1.68e+01 bond pdb=" O3P TPO A 911 " pdb=" P TPO A 911 " ideal model delta sigma weight residual 1.528 1.479 0.049 2.00e-02 2.50e+03 5.97e+00 bond pdb=" CB CYS A1017 " pdb=" SG CYS A1017 " ideal model delta sigma weight residual 1.808 1.866 -0.058 3.30e-02 9.18e+02 3.14e+00 ... (remaining 22017 not shown) Histogram of bond angle deviations from ideal: 99.96 - 106.78: 691 106.78 - 113.60: 25762 113.60 - 120.42: 7431 120.42 - 127.24: 5807 127.24 - 134.05: 113 Bond angle restraints: 39804 Sorted by residual: angle pdb=" CB TPO A 911 " pdb=" OG1 TPO A 911 " pdb=" P TPO A 911 " ideal model delta sigma weight residual 119.31 109.18 10.13 3.00e+00 1.11e-01 1.14e+01 angle pdb=" OG1 TPO A 911 " pdb=" P TPO A 911 " pdb=" O1P TPO A 911 " ideal model delta sigma weight residual 100.43 109.65 -9.22 3.00e+00 1.11e-01 9.45e+00 angle pdb=" C LEU A 559 " pdb=" N THR A 560 " pdb=" CA THR A 560 " ideal model delta sigma weight residual 122.61 127.34 -4.73 1.56e+00 4.11e-01 9.19e+00 angle pdb=" CA ARG A 638 " pdb=" CB ARG A 638 " pdb=" CG ARG A 638 " ideal model delta sigma weight residual 114.10 120.07 -5.97 2.00e+00 2.50e-01 8.92e+00 angle pdb=" CA LEU A 135 " pdb=" CB LEU A 135 " pdb=" CG LEU A 135 " ideal model delta sigma weight residual 116.30 126.50 -10.20 3.50e+00 8.16e-02 8.49e+00 ... (remaining 39799 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.08: 9212 17.08 - 34.16: 824 34.16 - 51.24: 189 51.24 - 68.32: 88 68.32 - 85.40: 12 Dihedral angle restraints: 10325 sinusoidal: 5523 harmonic: 4802 Sorted by residual: dihedral pdb=" CA SER A 846 " pdb=" C SER A 846 " pdb=" N PRO A 847 " pdb=" CA PRO A 847 " ideal model delta harmonic sigma weight residual 180.00 -156.05 -23.95 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA ILE A1352 " pdb=" C ILE A1352 " pdb=" N PRO A1353 " pdb=" CA PRO A1353 " ideal model delta harmonic sigma weight residual -180.00 -156.45 -23.55 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA CYS A 546 " pdb=" C CYS A 546 " pdb=" N THR A 547 " pdb=" CA THR A 547 " ideal model delta harmonic sigma weight residual 180.00 -160.29 -19.71 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 10322 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1240 0.036 - 0.072: 368 0.072 - 0.109: 123 0.109 - 0.145: 36 0.145 - 0.181: 5 Chirality restraints: 1772 Sorted by residual: chirality pdb=" CA VAL A 624 " pdb=" N VAL A 624 " pdb=" C VAL A 624 " pdb=" CB VAL A 624 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.19e-01 chirality pdb=" CA ILE A 626 " pdb=" N ILE A 626 " pdb=" C ILE A 626 " pdb=" CB ILE A 626 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.28e-01 chirality pdb=" CA ILE A1352 " pdb=" N ILE A1352 " pdb=" C ILE A1352 " pdb=" CB ILE A1352 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.50e-01 ... (remaining 1769 not shown) Planarity restraints: 3222 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 576 " 0.048 5.00e-02 4.00e+02 7.31e-02 8.55e+00 pdb=" N PRO A 577 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO A 577 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 577 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 304 " -0.043 5.00e-02 4.00e+02 6.57e-02 6.91e+00 pdb=" N PRO A 305 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 305 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 305 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A1126 " -0.036 5.00e-02 4.00e+02 5.37e-02 4.62e+00 pdb=" N PRO A1127 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A1127 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A1127 " -0.030 5.00e-02 4.00e+02 ... (remaining 3219 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.31: 4636 2.31 - 2.89: 48721 2.89 - 3.46: 54443 3.46 - 4.03: 69363 4.03 - 4.60: 105994 Nonbonded interactions: 283157 Sorted by model distance: nonbonded pdb=" O LEU A 802 " pdb=" HZ3 LYS A 807 " model vdw 1.743 1.850 nonbonded pdb=" O GLY A 797 " pdb=" H GLY A 800 " model vdw 1.763 1.850 nonbonded pdb=" O VAL A1447 " pdb=" HG1 THR A1451 " model vdw 1.768 1.850 nonbonded pdb=" O ALA A 278 " pdb=" HG1 THR A 282 " model vdw 1.779 1.850 nonbonded pdb=" O ILE A1097 " pdb=" HG SER A1100 " model vdw 1.780 1.850 ... (remaining 283152 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 group one per residue 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: 1.780 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: 6.930 Check model and map are aligned: 0.350 Set scattering table: 0.190 Process input model: 68.430 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 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 : 0.005 0.106 11103 Z= 0.317 Angle : 0.749 10.200 15067 Z= 0.398 Chirality : 0.042 0.181 1772 Planarity : 0.005 0.073 1879 Dihedral : 13.487 85.370 3985 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.60 % Allowed : 9.52 % Favored : 89.88 % 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 (0.22), residues: 1371 helix: 1.01 (0.16), residues: 925 sheet: -0.93 (0.61), residues: 54 loop : -2.53 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1014 HIS 0.005 0.001 HIS A 364 PHE 0.032 0.002 PHE A 548 TYR 0.027 0.002 TYR A 991 ARG 0.003 0.000 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 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 VAL 104 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 THR 179 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 LEU 497 is missing expected H atoms. Skipping. Residue LEU 525 is missing expected H atoms. Skipping. Residue MET 529 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 ILE 661 is missing expected H atoms. Skipping. Residue LEU 802 is missing expected H atoms. Skipping. Residue LYS 933 is missing expected H atoms. Skipping. Residue MET 962 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 LYS 1457 is missing expected H atoms. Skipping. Evaluate side-chains 373 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 366 time to evaluate : 1.769 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: A 27 ASP cc_start: 0.8713 (t0) cc_final: 0.8397 (t0) REVERT: A 81 LEU cc_start: 0.9231 (tt) cc_final: 0.9022 (tt) REVERT: A 142 GLU cc_start: 0.8582 (tp30) cc_final: 0.7925 (tt0) REVERT: A 245 LYS cc_start: 0.8489 (mttt) cc_final: 0.8174 (mttt) REVERT: A 453 ILE cc_start: 0.8419 (mt) cc_final: 0.8142 (tp) REVERT: A 532 THR cc_start: 0.8144 (m) cc_final: 0.7910 (p) REVERT: A 574 LEU cc_start: 0.8815 (tt) cc_final: 0.8504 (tt) REVERT: A 583 MET cc_start: 0.8932 (tmm) cc_final: 0.8565 (tmm) REVERT: A 967 MET cc_start: 0.8270 (mmp) cc_final: 0.8001 (mmt) REVERT: A 1107 GLN cc_start: 0.8649 (tm-30) cc_final: 0.8071 (tm-30) REVERT: A 1178 TYR cc_start: 0.8354 (t80) cc_final: 0.7987 (t80) REVERT: A 1194 LEU cc_start: 0.8513 (tp) cc_final: 0.8231 (mp) REVERT: A 1234 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8165 (tm-30) outliers start: 7 outliers final: 4 residues processed: 372 average time/residue: 0.4651 time to fit residues: 249.2469 Evaluate side-chains 237 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 233 time to evaluate : 1.777 ------------------------------------------------------------------------------- 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: 0.3980 chunk 105 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 71 optimal weight: 8.9990 chunk 56 optimal weight: 7.9990 chunk 108 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 126 optimal weight: 20.0000 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 ASN A 424 ASN A 790 HIS ** A1051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11103 Z= 0.221 Angle : 0.557 5.201 15067 Z= 0.322 Chirality : 0.037 0.149 1772 Planarity : 0.005 0.046 1879 Dihedral : 5.230 81.584 1498 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.09 % Allowed : 2.49 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.23), residues: 1371 helix: 1.13 (0.17), residues: 919 sheet: -0.72 (0.62), residues: 55 loop : -2.21 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1175 HIS 0.018 0.001 HIS A 790 PHE 0.021 0.002 PHE A1016 TYR 0.016 0.001 TYR A1215 ARG 0.002 0.000 ARG A 597 *********************** 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 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 VAL 104 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 THR 179 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 LEU 497 is missing expected H atoms. Skipping. Residue LEU 525 is missing expected H atoms. Skipping. Residue MET 529 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 ILE 661 is missing expected H atoms. Skipping. Residue LEU 802 is missing expected H atoms. Skipping. Residue LYS 933 is missing expected H atoms. Skipping. Residue MET 962 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 LYS 1457 is missing expected H atoms. Skipping. Evaluate side-chains 271 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 270 time to evaluate : 1.826 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: A 142 GLU cc_start: 0.8579 (tp30) cc_final: 0.7911 (tt0) REVERT: A 226 MET cc_start: 0.7938 (mmm) cc_final: 0.7572 (mmm) REVERT: A 245 LYS cc_start: 0.8470 (mttt) cc_final: 0.8246 (mttt) REVERT: A 298 ASP cc_start: 0.8518 (m-30) cc_final: 0.8094 (m-30) REVERT: A 453 ILE cc_start: 0.8476 (mt) cc_final: 0.8149 (tp) REVERT: A 532 THR cc_start: 0.8347 (m) cc_final: 0.8129 (p) REVERT: A 583 MET cc_start: 0.9005 (tmm) cc_final: 0.8528 (tmm) REVERT: A 1178 TYR cc_start: 0.8438 (t80) cc_final: 0.7723 (t80) REVERT: A 1234 GLU cc_start: 0.8726 (tm-30) cc_final: 0.8163 (tm-30) REVERT: A 1379 TRP cc_start: 0.6904 (t-100) cc_final: 0.6363 (t60) outliers start: 1 outliers final: 0 residues processed: 271 average time/residue: 0.4434 time to fit residues: 180.8333 Evaluate side-chains 215 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 1.803 ------------------------------------------------------------------------------- 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: 6.9990 chunk 39 optimal weight: 0.9980 chunk 105 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 126 optimal weight: 10.0000 chunk 136 optimal weight: 10.0000 chunk 112 optimal weight: 7.9990 chunk 125 optimal weight: 20.0000 chunk 43 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 ASN ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 648 ASN A 928 HIS A1055 ASN ** A1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1155 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 11103 Z= 0.282 Angle : 0.570 6.020 15067 Z= 0.326 Chirality : 0.038 0.157 1772 Planarity : 0.004 0.040 1879 Dihedral : 5.144 76.778 1498 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % 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: -0.47 (0.22), residues: 1371 helix: 0.56 (0.17), residues: 915 sheet: -1.06 (0.62), residues: 52 loop : -2.16 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 139 HIS 0.004 0.001 HIS A 364 PHE 0.039 0.002 PHE A 996 TYR 0.021 0.002 TYR A 991 ARG 0.003 0.000 ARG A1228 *********************** 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 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 VAL 104 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 THR 179 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 LEU 497 is missing expected H atoms. Skipping. Residue LEU 525 is missing expected H atoms. Skipping. Residue MET 529 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 ILE 661 is missing expected H atoms. Skipping. Residue LEU 802 is missing expected H atoms. Skipping. Residue LYS 933 is missing expected H atoms. Skipping. Residue MET 962 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 LYS 1457 is missing expected H atoms. Skipping. Evaluate side-chains 267 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 267 time to evaluate : 1.765 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 138 TYR cc_start: 0.8256 (t80) cc_final: 0.7873 (t80) REVERT: A 142 GLU cc_start: 0.8289 (tp30) cc_final: 0.7801 (tt0) REVERT: A 245 LYS cc_start: 0.8504 (mttt) cc_final: 0.8243 (mttt) REVERT: A 298 ASP cc_start: 0.8722 (m-30) cc_final: 0.8289 (m-30) REVERT: A 583 MET cc_start: 0.8952 (tmm) cc_final: 0.8448 (tmm) REVERT: A 698 GLN cc_start: 0.9388 (pm20) cc_final: 0.9158 (pm20) REVERT: A 967 MET cc_start: 0.7997 (mmt) cc_final: 0.7367 (mmt) REVERT: A 1178 TYR cc_start: 0.8506 (t80) cc_final: 0.8014 (t80) REVERT: A 1234 GLU cc_start: 0.8689 (tm-30) cc_final: 0.8149 (tm-30) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.4105 time to fit residues: 166.5120 Evaluate side-chains 213 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 1.649 ------------------------------------------------------------------------------- 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: 20.0000 chunk 95 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 126 optimal weight: 20.0000 chunk 134 optimal weight: 20.0000 chunk 66 optimal weight: 9.9990 chunk 120 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1070 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11103 Z= 0.215 Angle : 0.514 5.143 15067 Z= 0.293 Chirality : 0.036 0.152 1772 Planarity : 0.004 0.037 1879 Dihedral : 4.993 74.320 1498 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % 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: -0.62 (0.22), residues: 1371 helix: 0.47 (0.17), residues: 916 sheet: -0.76 (0.59), residues: 65 loop : -2.41 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1014 HIS 0.003 0.001 HIS A1466 PHE 0.049 0.002 PHE A 996 TYR 0.020 0.001 TYR A 991 ARG 0.002 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 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 VAL 104 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 THR 179 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 LEU 497 is missing expected H atoms. Skipping. Residue LEU 525 is missing expected H atoms. Skipping. Residue MET 529 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 ILE 661 is missing expected H atoms. Skipping. Residue LEU 802 is missing expected H atoms. Skipping. Residue LYS 933 is missing expected H atoms. Skipping. Residue MET 962 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 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: 0 poor density : 264 time to evaluate : 1.930 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 138 TYR cc_start: 0.8219 (t80) cc_final: 0.7828 (t80) REVERT: A 142 GLU cc_start: 0.8350 (tp30) cc_final: 0.7839 (tt0) REVERT: A 245 LYS cc_start: 0.8522 (mttt) cc_final: 0.8274 (mttt) REVERT: A 288 LEU cc_start: 0.8390 (tp) cc_final: 0.8186 (tt) REVERT: A 298 ASP cc_start: 0.8603 (m-30) cc_final: 0.8323 (m-30) REVERT: A 583 MET cc_start: 0.8983 (tmm) cc_final: 0.8496 (tmm) REVERT: A 698 GLN cc_start: 0.9397 (pm20) cc_final: 0.9104 (pm20) REVERT: A 967 MET cc_start: 0.7933 (mmt) cc_final: 0.7371 (mmt) REVERT: A 969 ASN cc_start: 0.8602 (t0) cc_final: 0.8359 (t0) REVERT: A 1029 MET cc_start: 0.7605 (tpt) cc_final: 0.7267 (tpt) REVERT: A 1178 TYR cc_start: 0.8514 (t80) cc_final: 0.8211 (t80) REVERT: A 1234 GLU cc_start: 0.8663 (tm-30) cc_final: 0.8200 (tm-30) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.4648 time to fit residues: 189.6874 Evaluate side-chains 212 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 1.878 ------------------------------------------------------------------------------- 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: 8.9990 chunk 76 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 100 optimal weight: 7.9990 chunk 55 optimal weight: 0.0570 chunk 114 optimal weight: 8.9990 chunk 92 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 68 optimal weight: 8.9990 chunk 120 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 overall best weight: 6.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.4565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 11103 Z= 0.294 Angle : 0.590 7.374 15067 Z= 0.336 Chirality : 0.038 0.158 1772 Planarity : 0.004 0.036 1879 Dihedral : 5.101 70.565 1498 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % 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: -1.01 (0.22), residues: 1371 helix: 0.12 (0.17), residues: 916 sheet: -0.68 (0.62), residues: 63 loop : -2.44 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 139 HIS 0.006 0.001 HIS A 364 PHE 0.058 0.002 PHE A 996 TYR 0.022 0.002 TYR A1109 ARG 0.003 0.000 ARG A 906 *********************** 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 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 VAL 104 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 THR 179 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 LEU 497 is missing expected H atoms. Skipping. Residue LEU 525 is missing expected H atoms. Skipping. Residue MET 529 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 ILE 661 is missing expected H atoms. Skipping. Residue LEU 802 is missing expected H atoms. Skipping. Residue LYS 933 is missing expected H atoms. Skipping. Residue MET 962 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 LYS 1457 is missing expected H atoms. Skipping. Evaluate side-chains 259 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 1.722 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: A 138 TYR cc_start: 0.8483 (t80) cc_final: 0.7696 (t80) REVERT: A 142 GLU cc_start: 0.8536 (tp30) cc_final: 0.7856 (mm-30) REVERT: A 180 CYS cc_start: 0.8711 (m) cc_final: 0.8289 (m) REVERT: A 583 MET cc_start: 0.8925 (tmm) cc_final: 0.8422 (tmm) REVERT: A 698 GLN cc_start: 0.9478 (pm20) cc_final: 0.9149 (pm20) REVERT: A 1234 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8237 (tm-30) REVERT: A 1243 ILE cc_start: 0.9185 (tp) cc_final: 0.8864 (tp) outliers start: 0 outliers final: 0 residues processed: 259 average time/residue: 0.3976 time to fit residues: 159.2229 Evaluate side-chains 216 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 1.734 ------------------------------------------------------------------------------- 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: 0.9990 chunk 120 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 78 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 chunk 134 optimal weight: 20.0000 chunk 111 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 GLN A1020 HIS ** A1366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11103 Z= 0.163 Angle : 0.502 5.688 15067 Z= 0.282 Chirality : 0.036 0.152 1772 Planarity : 0.004 0.033 1879 Dihedral : 4.860 69.668 1498 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % 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: -0.69 (0.23), residues: 1371 helix: 0.39 (0.17), residues: 919 sheet: -0.79 (0.59), residues: 65 loop : -2.39 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1014 HIS 0.003 0.001 HIS A 364 PHE 0.046 0.001 PHE A 996 TYR 0.019 0.001 TYR A 991 ARG 0.002 0.000 ARG A1380 *********************** 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 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 VAL 104 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 THR 179 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 LEU 497 is missing expected H atoms. Skipping. Residue LEU 525 is missing expected H atoms. Skipping. Residue MET 529 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 ILE 661 is missing expected H atoms. Skipping. Residue LEU 802 is missing expected H atoms. Skipping. Residue LYS 933 is missing expected H atoms. Skipping. Residue MET 962 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 LYS 1457 is missing expected H atoms. Skipping. Evaluate side-chains 271 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 271 time to evaluate : 1.678 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: A 27 ASP cc_start: 0.8846 (t0) cc_final: 0.8439 (t0) REVERT: A 138 TYR cc_start: 0.8304 (t80) cc_final: 0.7402 (t80) REVERT: A 142 GLU cc_start: 0.8470 (tp30) cc_final: 0.7820 (mm-30) REVERT: A 583 MET cc_start: 0.8980 (tmm) cc_final: 0.8460 (tmm) REVERT: A 698 GLN cc_start: 0.9500 (pm20) cc_final: 0.9130 (pm20) REVERT: A 967 MET cc_start: 0.7772 (mmt) cc_final: 0.7324 (mmt) REVERT: A 969 ASN cc_start: 0.8606 (t0) cc_final: 0.8290 (t0) REVERT: A 1029 MET cc_start: 0.7634 (tpt) cc_final: 0.7419 (tpt) REVERT: A 1178 TYR cc_start: 0.8575 (t80) cc_final: 0.8236 (t80) REVERT: A 1234 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8223 (tm-30) REVERT: A 1243 ILE cc_start: 0.9157 (tp) cc_final: 0.8884 (tp) REVERT: A 1359 PHE cc_start: 0.8946 (m-80) cc_final: 0.8650 (m-10) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.4072 time to fit residues: 168.0269 Evaluate side-chains 214 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 1.539 ------------------------------------------------------------------------------- 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: 10.0000 chunk 15 optimal weight: 0.7980 chunk 76 optimal weight: 10.0000 chunk 98 optimal weight: 0.8980 chunk 113 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 chunk 133 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 overall best weight: 4.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 ASN ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1020 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.4923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11103 Z= 0.232 Angle : 0.540 6.971 15067 Z= 0.303 Chirality : 0.037 0.161 1772 Planarity : 0.004 0.035 1879 Dihedral : 4.919 67.896 1498 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % 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: -0.70 (0.22), residues: 1371 helix: 0.40 (0.17), residues: 907 sheet: -0.62 (0.61), residues: 63 loop : -2.38 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 225 HIS 0.004 0.001 HIS A1390 PHE 0.032 0.002 PHE A 996 TYR 0.019 0.002 TYR A 991 ARG 0.008 0.000 ARG A1115 *********************** 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 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 VAL 104 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 THR 179 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 LEU 497 is missing expected H atoms. Skipping. Residue LEU 525 is missing expected H atoms. Skipping. Residue MET 529 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 ILE 661 is missing expected H atoms. Skipping. Residue LEU 802 is missing expected H atoms. Skipping. Residue LYS 933 is missing expected H atoms. Skipping. Residue MET 962 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 LYS 1457 is missing expected H atoms. Skipping. Evaluate side-chains 257 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 1.758 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: 0.8896 (t0) cc_final: 0.8478 (t0) REVERT: A 138 TYR cc_start: 0.8439 (t80) cc_final: 0.7575 (t80) REVERT: A 142 GLU cc_start: 0.8594 (tp30) cc_final: 0.8111 (mm-30) REVERT: A 583 MET cc_start: 0.8888 (tmm) cc_final: 0.8469 (tmm) REVERT: A 698 GLN cc_start: 0.9484 (pm20) cc_final: 0.9132 (pm20) REVERT: A 923 ILE cc_start: 0.7788 (mt) cc_final: 0.7220 (tp) REVERT: A 967 MET cc_start: 0.7897 (mmt) cc_final: 0.7493 (mmt) REVERT: A 1004 LEU cc_start: 0.9058 (tt) cc_final: 0.8831 (tt) REVERT: A 1029 MET cc_start: 0.7715 (tpt) cc_final: 0.7082 (tpt) REVERT: A 1234 GLU cc_start: 0.8787 (tm-30) cc_final: 0.8204 (tm-30) REVERT: A 1243 ILE cc_start: 0.9163 (tp) cc_final: 0.8287 (tp) REVERT: A 1359 PHE cc_start: 0.9002 (m-80) cc_final: 0.8656 (m-10) outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.4051 time to fit residues: 159.1614 Evaluate side-chains 214 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 1.768 ------------------------------------------------------------------------------- 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: 5.9990 chunk 80 optimal weight: 10.0000 chunk 40 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 105 optimal weight: 0.9990 chunk 121 optimal weight: 7.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.4942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11103 Z= 0.150 Angle : 0.495 5.618 15067 Z= 0.276 Chirality : 0.036 0.149 1772 Planarity : 0.004 0.058 1879 Dihedral : 4.768 67.566 1498 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % 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: -0.48 (0.23), residues: 1371 helix: 0.60 (0.17), residues: 910 sheet: -0.79 (0.59), residues: 65 loop : -2.35 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 975 HIS 0.003 0.001 HIS A 364 PHE 0.034 0.001 PHE A 996 TYR 0.030 0.001 TYR A 991 ARG 0.004 0.000 ARG A 990 *********************** 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 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 VAL 104 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 THR 179 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 LEU 497 is missing expected H atoms. Skipping. Residue LEU 525 is missing expected H atoms. Skipping. Residue MET 529 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 ILE 661 is missing expected H atoms. Skipping. Residue LEU 802 is missing expected H atoms. Skipping. Residue LYS 933 is missing expected H atoms. Skipping. Residue MET 962 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 LYS 1457 is missing expected H atoms. Skipping. Evaluate side-chains 266 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 266 time to evaluate : 1.642 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: 0.8837 (t0) cc_final: 0.8452 (t0) REVERT: A 138 TYR cc_start: 0.8348 (t80) cc_final: 0.7473 (t80) REVERT: A 142 GLU cc_start: 0.8530 (tp30) cc_final: 0.8067 (mm-30) REVERT: A 583 MET cc_start: 0.8921 (tmm) cc_final: 0.8513 (tmm) REVERT: A 698 GLN cc_start: 0.9475 (pm20) cc_final: 0.9133 (pm20) REVERT: A 967 MET cc_start: 0.7811 (mmt) cc_final: 0.7420 (mmt) REVERT: A 1029 MET cc_start: 0.7667 (tpt) cc_final: 0.7458 (tpt) REVERT: A 1178 TYR cc_start: 0.8562 (t80) cc_final: 0.8261 (t80) REVERT: A 1234 GLU cc_start: 0.8771 (tm-30) cc_final: 0.8258 (tm-30) REVERT: A 1243 ILE cc_start: 0.9158 (tp) cc_final: 0.8860 (tp) REVERT: A 1359 PHE cc_start: 0.8986 (m-80) cc_final: 0.8653 (m-10) outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.3931 time to fit residues: 161.3115 Evaluate side-chains 222 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 1.714 ------------------------------------------------------------------------------- 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: 10.0000 chunk 117 optimal weight: 0.0060 chunk 124 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 54 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 118 optimal weight: 9.9990 chunk 81 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 overall best weight: 2.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 979 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 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 : 0.002 0.026 11103 Z= 0.156 Angle : 0.489 5.518 15067 Z= 0.273 Chirality : 0.036 0.155 1772 Planarity : 0.004 0.042 1879 Dihedral : 4.679 67.169 1498 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % 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: -0.34 (0.23), residues: 1371 helix: 0.73 (0.18), residues: 905 sheet: -0.83 (0.59), residues: 65 loop : -2.32 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 975 HIS 0.005 0.001 HIS A 364 PHE 0.031 0.001 PHE A 996 TYR 0.015 0.001 TYR A 991 ARG 0.008 0.000 ARG A 990 *********************** 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 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 VAL 104 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 THR 179 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 LEU 497 is missing expected H atoms. Skipping. Residue LEU 525 is missing expected H atoms. Skipping. Residue MET 529 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 ILE 661 is missing expected H atoms. Skipping. Residue LEU 802 is missing expected H atoms. Skipping. Residue LYS 933 is missing expected H atoms. Skipping. Residue MET 962 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 LYS 1457 is missing expected H atoms. Skipping. Evaluate side-chains 267 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 267 time to evaluate : 1.707 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: A 27 ASP cc_start: 0.8815 (t0) cc_final: 0.8403 (t0) REVERT: A 138 TYR cc_start: 0.8349 (t80) cc_final: 0.7629 (t80) REVERT: A 142 GLU cc_start: 0.8535 (tp30) cc_final: 0.8084 (mm-30) REVERT: A 583 MET cc_start: 0.8967 (tmm) cc_final: 0.8542 (tmm) REVERT: A 698 GLN cc_start: 0.9470 (pm20) cc_final: 0.9143 (pm20) REVERT: A 923 ILE cc_start: 0.7756 (mt) cc_final: 0.7182 (tp) REVERT: A 958 ILE cc_start: 0.9074 (tp) cc_final: 0.8672 (tt) REVERT: A 967 MET cc_start: 0.7806 (mmt) cc_final: 0.7417 (mmt) REVERT: A 1004 LEU cc_start: 0.9063 (tt) cc_final: 0.8854 (tt) REVERT: A 1029 MET cc_start: 0.7675 (tpt) cc_final: 0.7445 (tpt) REVERT: A 1234 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8270 (tm-30) REVERT: A 1243 ILE cc_start: 0.9208 (tp) cc_final: 0.8915 (tp) REVERT: A 1359 PHE cc_start: 0.8988 (m-80) cc_final: 0.8644 (m-10) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.4060 time to fit residues: 166.2149 Evaluate side-chains 221 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 1.688 ------------------------------------------------------------------------------- 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: 4.9990 chunk 62 optimal weight: 20.0000 chunk 91 optimal weight: 9.9990 chunk 138 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 110 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 67 optimal weight: 8.9990 chunk 87 optimal weight: 6.9990 chunk 117 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 979 ASN A1020 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.5208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11103 Z= 0.222 Angle : 0.533 7.464 15067 Z= 0.301 Chirality : 0.037 0.181 1772 Planarity : 0.004 0.044 1879 Dihedral : 4.800 66.526 1498 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: -0.55 (0.23), residues: 1371 helix: 0.56 (0.17), residues: 909 sheet: -0.81 (0.60), residues: 65 loop : -2.40 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 975 HIS 0.004 0.001 HIS A1390 PHE 0.041 0.002 PHE A 957 TYR 0.014 0.002 TYR A1109 ARG 0.009 0.000 ARG A 990 ********************** 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 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 VAL 104 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 THR 179 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 LEU 497 is missing expected H atoms. Skipping. Residue LEU 525 is missing expected H atoms. Skipping. Residue MET 529 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 ILE 661 is missing expected H atoms. Skipping. Residue LEU 802 is missing expected H atoms. Skipping. Residue LYS 933 is missing expected H atoms. Skipping. Residue MET 962 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 LYS 1457 is missing expected H atoms. Skipping. Evaluate side-chains 259 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 1.713 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: A 27 ASP cc_start: 0.8860 (t0) cc_final: 0.8638 (t0) REVERT: A 138 TYR cc_start: 0.8481 (t80) cc_final: 0.7524 (t80) REVERT: A 142 GLU cc_start: 0.8574 (tp30) cc_final: 0.8105 (mm-30) REVERT: A 583 MET cc_start: 0.8961 (tmm) cc_final: 0.8486 (tmm) REVERT: A 698 GLN cc_start: 0.9501 (pm20) cc_final: 0.9140 (pm20) REVERT: A 923 ILE cc_start: 0.7732 (mt) cc_final: 0.7190 (tp) REVERT: A 958 ILE cc_start: 0.9042 (tp) cc_final: 0.8779 (tt) REVERT: A 967 MET cc_start: 0.7839 (mmt) cc_final: 0.7459 (mmt) REVERT: A 1029 MET cc_start: 0.7671 (tpt) cc_final: 0.7053 (tpt) REVERT: A 1234 GLU cc_start: 0.8781 (tm-30) cc_final: 0.8285 (tm-30) REVERT: A 1243 ILE cc_start: 0.9179 (tp) cc_final: 0.8234 (tp) REVERT: A 1359 PHE cc_start: 0.9037 (m-80) cc_final: 0.8623 (m-10) REVERT: A 1379 TRP cc_start: 0.6821 (t-100) cc_final: 0.6177 (t60) outliers start: 0 outliers final: 0 residues processed: 259 average time/residue: 0.4318 time to fit residues: 170.9218 Evaluate side-chains 216 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 1.867 ------------------------------------------------------------------------------- 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: 7.9990 chunk 101 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 110 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 chunk 113 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 979 ASN A1020 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.140230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.115871 restraints weight = 78209.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.120727 restraints weight = 32213.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.123683 restraints weight = 17499.505| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3779 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3779 r_free = 0.3779 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3778 r_free = 0.3778 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.5216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11103 Z= 0.176 Angle : 0.497 5.517 15067 Z= 0.279 Chirality : 0.036 0.155 1772 Planarity : 0.004 0.036 1879 Dihedral : 4.743 65.996 1498 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % 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: -0.40 (0.23), residues: 1371 helix: 0.68 (0.18), residues: 903 sheet: -0.82 (0.59), residues: 65 loop : -2.32 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 975 HIS 0.004 0.001 HIS A 364 PHE 0.031 0.001 PHE A 957 TYR 0.013 0.001 TYR A1109 ARG 0.007 0.000 ARG A 990 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4541.71 seconds wall clock time: 81 minutes 22.16 seconds (4882.16 seconds total)