Starting phenix.real_space_refine on Wed Feb 14 23:55:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yud_6845/02_2024/5yud_6845_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yud_6845/02_2024/5yud_6845.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yud_6845/02_2024/5yud_6845.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yud_6845/02_2024/5yud_6845.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yud_6845/02_2024/5yud_6845_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yud_6845/02_2024/5yud_6845_neut_updated.pdb" } resolution = 4.28 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 44 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 54 5.16 5 C 6691 2.51 5 N 1779 2.21 5 O 1983 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 150": "NH1" <-> "NH2" Residue "A ARG 482": "NH1" <-> "NH2" Residue "A PHE 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 736": "NH1" <-> "NH2" Residue "A ARG 846": "NH1" <-> "NH2" Residue "A ARG 1110": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10510 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 9943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1238, 9943 Classifications: {'peptide': 1238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 50, 'TRANS': 1187} Chain breaks: 1 Chain: "C" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 536 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.01, per 1000 atoms: 0.57 Number of scatterers: 10510 At special positions: 0 Unit cell: (92.7643, 118.895, 138.493, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 54 16.00 P 3 15.00 O 1983 8.00 N 1779 7.00 C 6691 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.64 Conformation dependent library (CDL) restraints added in 1.9 seconds 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2510 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 59 helices and 6 sheets defined 42.0% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.95 Creating SS restraints... Processing helix chain 'A' and resid 23 through 25 No H-bonds generated for 'chain 'A' and resid 23 through 25' Processing helix chain 'A' and resid 27 through 30 No H-bonds generated for 'chain 'A' and resid 27 through 30' Processing helix chain 'A' and resid 37 through 50 removed outlier: 4.072A pdb=" N HIS A 43 " --> pdb=" O GLU A 39 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LYS A 44 " --> pdb=" O GLU A 40 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU A 45 " --> pdb=" O GLU A 41 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS A 50 " --> pdb=" O ARG A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 67 removed outlier: 4.102A pdb=" N LEU A 64 " --> pdb=" O ALA A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 84 removed outlier: 3.728A pdb=" N ALA A 83 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 120 Processing helix chain 'A' and resid 143 through 148 removed outlier: 4.119A pdb=" N LYS A 147 " --> pdb=" O LYS A 143 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N MET A 148 " --> pdb=" O ARG A 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 143 through 148' Processing helix chain 'A' and resid 159 through 167 removed outlier: 4.038A pdb=" N SER A 165 " --> pdb=" O ALA A 161 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE A 166 " --> pdb=" O ARG A 162 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 183 Processing helix chain 'A' and resid 213 through 220 removed outlier: 5.303A pdb=" N ALA A 218 " --> pdb=" O TRP A 214 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LYS A 219 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 228 No H-bonds generated for 'chain 'A' and resid 225 through 228' Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.677A pdb=" N GLN A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 417 removed outlier: 3.676A pdb=" N TYR A 411 " --> pdb=" O LEU A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 460 removed outlier: 3.711A pdb=" N SER A 460 " --> pdb=" O PRO A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 488 removed outlier: 3.922A pdb=" N LEU A 480 " --> pdb=" O LYS A 476 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE A 483 " --> pdb=" O PHE A 479 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA A 484 " --> pdb=" O LEU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 497 removed outlier: 3.832A pdb=" N ARG A 497 " --> pdb=" O PRO A 493 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 493 through 497' Processing helix chain 'A' and resid 508 through 511 Proline residue: A 511 - end of helix No H-bonds generated for 'chain 'A' and resid 508 through 511' Processing helix chain 'A' and resid 516 through 523 Processing helix chain 'A' and resid 532 through 541 removed outlier: 4.327A pdb=" N SER A 537 " --> pdb=" O VAL A 533 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N SER A 538 " --> pdb=" O CYS A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 589 removed outlier: 4.773A pdb=" N ARG A 587 " --> pdb=" O ASN A 584 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASP A 588 " --> pdb=" O ARG A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 614 Processing helix chain 'A' and resid 621 through 630 removed outlier: 3.971A pdb=" N ILE A 626 " --> pdb=" O VAL A 622 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE A 627 " --> pdb=" O GLU A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 636 No H-bonds generated for 'chain 'A' and resid 633 through 636' Processing helix chain 'A' and resid 642 through 650 Processing helix chain 'A' and resid 665 through 679 removed outlier: 3.696A pdb=" N GLN A 673 " --> pdb=" O GLN A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 702 removed outlier: 3.581A pdb=" N GLN A 695 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LEU A 696 " --> pdb=" O SER A 692 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA A 697 " --> pdb=" O CYS A 693 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR A 699 " --> pdb=" O GLN A 695 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY A 700 " --> pdb=" O LEU A 696 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LEU A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE A 702 " --> pdb=" O LEU A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 716 Processing helix chain 'A' and resid 724 through 728 removed outlier: 4.212A pdb=" N LEU A 728 " --> pdb=" O LEU A 724 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 724 through 728' Processing helix chain 'A' and resid 746 through 759 removed outlier: 3.755A pdb=" N ALA A 754 " --> pdb=" O GLU A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 778 removed outlier: 3.798A pdb=" N ARG A 777 " --> pdb=" O LEU A 773 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN A 778 " --> pdb=" O TYR A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 786 Processing helix chain 'A' and resid 790 through 799 removed outlier: 3.549A pdb=" N TYR A 794 " --> pdb=" O ASN A 790 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR A 795 " --> pdb=" O ILE A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 813 Proline residue: A 806 - end of helix removed outlier: 3.684A pdb=" N HIS A 811 " --> pdb=" O THR A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 834 Processing helix chain 'A' and resid 837 through 851 Processing helix chain 'A' and resid 853 through 873 removed outlier: 3.764A pdb=" N SER A 857 " --> pdb=" O PRO A 853 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A 862 " --> pdb=" O SER A 858 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N HIS A 863 " --> pdb=" O PHE A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 889 Proline residue: A 883 - end of helix removed outlier: 3.624A pdb=" N GLN A 887 " --> pdb=" O PRO A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 901 removed outlier: 3.898A pdb=" N ASN A 900 " --> pdb=" O ARG A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 938 removed outlier: 4.578A pdb=" N TYR A 937 " --> pdb=" O PHE A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 977 removed outlier: 3.923A pdb=" N ILE A 970 " --> pdb=" O GLN A 966 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR A 974 " --> pdb=" O ILE A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 992 No H-bonds generated for 'chain 'A' and resid 989 through 992' Processing helix chain 'A' and resid 1009 through 1011 No H-bonds generated for 'chain 'A' and resid 1009 through 1011' Processing helix chain 'A' and resid 1014 through 1024 removed outlier: 3.932A pdb=" N GLU A1022 " --> pdb=" O GLN A1018 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A1023 " --> pdb=" O VAL A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1040 through 1050 removed outlier: 3.514A pdb=" N CYS A1045 " --> pdb=" O LEU A1041 " (cutoff:3.500A) Proline residue: A1046 - end of helix removed outlier: 4.254A pdb=" N LEU A1050 " --> pdb=" O PRO A1046 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1068 No H-bonds generated for 'chain 'A' and resid 1066 through 1068' Processing helix chain 'A' and resid 1070 through 1075 Processing helix chain 'A' and resid 1119 through 1121 No H-bonds generated for 'chain 'A' and resid 1119 through 1121' Processing helix chain 'A' and resid 1144 through 1156 removed outlier: 4.114A pdb=" N GLN A1152 " --> pdb=" O VAL A1148 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ASN A1153 " --> pdb=" O LYS A1149 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE A1154 " --> pdb=" O PHE A1150 " (cutoff:3.500A) Proline residue: A1155 - end of helix Processing helix chain 'A' and resid 1173 through 1177 Processing helix chain 'A' and resid 1202 through 1204 No H-bonds generated for 'chain 'A' and resid 1202 through 1204' Processing helix chain 'A' and resid 1221 through 1233 Processing helix chain 'A' and resid 1248 through 1261 removed outlier: 3.905A pdb=" N LYS A1253 " --> pdb=" O GLN A1250 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N GLN A1258 " --> pdb=" O ILE A1255 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU A1260 " --> pdb=" O ARG A1257 " (cutoff:3.500A) Processing helix chain 'A' and resid 1278 through 1287 Processing helix chain 'A' and resid 1307 through 1313 removed outlier: 4.537A pdb=" N ARG A1311 " --> pdb=" O GLU A1308 " (cutoff:3.500A) Processing helix chain 'A' and resid 1338 through 1350 removed outlier: 5.460A pdb=" N GLY A1347 " --> pdb=" O LYS A1344 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN A1348 " --> pdb=" O ALA A1345 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N CYS A1349 " --> pdb=" O LEU A1346 " (cutoff:3.500A) Processing helix chain 'A' and resid 1365 through 1373 Processing helix chain 'A' and resid 1398 through 1401 Processing helix chain 'C' and resid 427 through 443 removed outlier: 4.757A pdb=" N ASN C 432 " --> pdb=" O GLY C 428 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER C 433 " --> pdb=" O LEU C 429 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA C 439 " --> pdb=" O LYS C 435 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE C 443 " --> pdb=" O ALA C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 494 removed outlier: 4.068A pdb=" N GLU C 462 " --> pdb=" O ASP C 458 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN C 473 " --> pdb=" O ALA C 469 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASN C 484 " --> pdb=" O LEU C 480 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N GLN C 485 " --> pdb=" O ALA C 481 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL C 486 " --> pdb=" O GLN C 482 " (cutoff:3.500A) Proline residue: C 487 - end of helix removed outlier: 4.077A pdb=" N LEU C 493 " --> pdb=" O ASN C 489 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU C 494 " --> pdb=" O VAL C 490 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 186 through 188 Processing sheet with id= B, first strand: chain 'A' and resid 502 through 504 removed outlier: 3.531A pdb=" N ASP A 551 " --> pdb=" O LEU A 504 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N CYS A 576 " --> pdb=" O PHE A 548 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N LEU A 550 " --> pdb=" O CYS A 576 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU A 578 " --> pdb=" O LEU A 550 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 892 through 895 Processing sheet with id= D, first strand: chain 'A' and resid 1032 through 1034 Processing sheet with id= E, first strand: chain 'A' and resid 1082 through 1084 Processing sheet with id= F, first strand: chain 'A' and resid 1296 through 1299 removed outlier: 6.003A pdb=" N GLU A1325 " --> pdb=" O LEU A1297 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ILE A1299 " --> pdb=" O GLU A1325 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ASN A1327 " --> pdb=" O ILE A1299 " (cutoff:3.500A) No H-bonds generated for sheet with id= F 262 hydrogen bonds defined for protein. 663 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.17 Time building geometry restraints manager: 4.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1766 1.31 - 1.44: 2799 1.44 - 1.56: 6082 1.56 - 1.69: 5 1.69 - 1.81: 75 Bond restraints: 10727 Sorted by residual: bond pdb=" C4 ATP A1501 " pdb=" C5 ATP A1501 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.35e+01 bond pdb=" C TRP A 76 " pdb=" N THR A 77 " ideal model delta sigma weight residual 1.331 1.190 0.141 2.07e-02 2.33e+03 4.63e+01 bond pdb=" C5 ATP A1501 " pdb=" C6 ATP A1501 " ideal model delta sigma weight residual 1.409 1.471 -0.062 1.00e-02 1.00e+04 3.82e+01 bond pdb=" C5 ATP A1501 " pdb=" N7 ATP A1501 " ideal model delta sigma weight residual 1.387 1.334 0.053 1.00e-02 1.00e+04 2.78e+01 bond pdb=" C4 ATP A1501 " pdb=" N9 ATP A1501 " ideal model delta sigma weight residual 1.374 1.327 0.047 1.00e-02 1.00e+04 2.25e+01 ... (remaining 10722 not shown) Histogram of bond angle deviations from ideal: 90.76 - 99.96: 9 99.96 - 109.16: 1093 109.16 - 118.36: 7306 118.36 - 127.55: 6001 127.55 - 136.75: 104 Bond angle restraints: 14513 Sorted by residual: angle pdb=" PB ATP A1501 " pdb=" O3B ATP A1501 " pdb=" PG ATP A1501 " ideal model delta sigma weight residual 139.87 112.34 27.53 1.00e+00 1.00e+00 7.58e+02 angle pdb=" C HIS A 907 " pdb=" N PRO A 908 " pdb=" CA PRO A 908 " ideal model delta sigma weight residual 119.84 94.12 25.72 1.25e+00 6.40e-01 4.23e+02 angle pdb=" N TYR A 903 " pdb=" CA TYR A 903 " pdb=" C TYR A 903 " ideal model delta sigma weight residual 113.41 90.76 22.65 1.22e+00 6.72e-01 3.45e+02 angle pdb=" PA ATP A1501 " pdb=" O3A ATP A1501 " pdb=" PB ATP A1501 " ideal model delta sigma weight residual 136.83 119.36 17.47 1.00e+00 1.00e+00 3.05e+02 angle pdb=" C5 ATP A1501 " pdb=" C4 ATP A1501 " pdb=" N3 ATP A1501 " ideal model delta sigma weight residual 126.80 118.70 8.10 1.00e+00 1.00e+00 6.56e+01 ... (remaining 14508 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.98: 6084 15.98 - 31.97: 398 31.97 - 47.95: 37 47.95 - 63.93: 9 63.93 - 79.92: 5 Dihedral angle restraints: 6533 sinusoidal: 2677 harmonic: 3856 Sorted by residual: dihedral pdb=" CA HIS A1381 " pdb=" C HIS A1381 " pdb=" N PRO A1382 " pdb=" CA PRO A1382 " ideal model delta harmonic sigma weight residual -180.00 -130.09 -49.91 0 5.00e+00 4.00e-02 9.96e+01 dihedral pdb=" CA GLN A 735 " pdb=" C GLN A 735 " pdb=" N ARG A 736 " pdb=" CA ARG A 736 " ideal model delta harmonic sigma weight residual 180.00 144.80 35.20 0 5.00e+00 4.00e-02 4.96e+01 dihedral pdb=" CA GLU A1141 " pdb=" C GLU A1141 " pdb=" N SER A1142 " pdb=" CA SER A1142 " ideal model delta harmonic sigma weight residual -180.00 -145.39 -34.61 0 5.00e+00 4.00e-02 4.79e+01 ... (remaining 6530 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1462 0.095 - 0.191: 159 0.191 - 0.286: 6 0.286 - 0.381: 0 0.381 - 0.477: 3 Chirality restraints: 1630 Sorted by residual: chirality pdb=" CA ASP A 947 " pdb=" N ASP A 947 " pdb=" C ASP A 947 " pdb=" CB ASP A 947 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.68e+00 chirality pdb=" CA TYR A 903 " pdb=" N TYR A 903 " pdb=" C TYR A 903 " pdb=" CB TYR A 903 " both_signs ideal model delta sigma weight residual False 2.51 2.93 -0.42 2.00e-01 2.50e+01 4.39e+00 chirality pdb=" CA ILE A1273 " pdb=" N ILE A1273 " pdb=" C ILE A1273 " pdb=" CB ILE A1273 " both_signs ideal model delta sigma weight residual False 2.43 2.02 0.42 2.00e-01 2.50e+01 4.32e+00 ... (remaining 1627 not shown) Planarity restraints: 1865 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 902 " -0.027 2.00e-02 2.50e+03 5.69e-02 3.23e+01 pdb=" C GLN A 902 " 0.098 2.00e-02 2.50e+03 pdb=" O GLN A 902 " -0.039 2.00e-02 2.50e+03 pdb=" N TYR A 903 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 907 " -0.095 5.00e-02 4.00e+02 1.40e-01 3.16e+01 pdb=" N PRO A 908 " 0.241 5.00e-02 4.00e+02 pdb=" CA PRO A 908 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 908 " -0.094 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 947 " 0.021 2.00e-02 2.50e+03 4.27e-02 1.83e+01 pdb=" C ASP A 947 " -0.074 2.00e-02 2.50e+03 pdb=" O ASP A 947 " 0.028 2.00e-02 2.50e+03 pdb=" N GLU A 948 " 0.025 2.00e-02 2.50e+03 ... (remaining 1862 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 11 2.02 - 2.74: 1730 2.74 - 3.46: 17035 3.46 - 4.18: 25845 4.18 - 4.90: 42216 Nonbonded interactions: 86837 Sorted by model distance: nonbonded pdb=" O ASP A 631 " pdb=" CD2 LEU A 635 " model vdw 1.301 3.460 nonbonded pdb=" OG SER A 59 " pdb=" CG1 VAL A 132 " model vdw 1.800 3.460 nonbonded pdb=" CD2 LEU A1274 " pdb=" CD1 ILE A1299 " model vdw 1.821 3.880 nonbonded pdb=" SG CYS A 467 " pdb=" CD2 LEU A 593 " model vdw 1.889 3.820 nonbonded pdb=" O ASP A 947 " pdb=" N TYR A 950 " model vdw 1.932 2.520 ... (remaining 86832 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=0.00 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: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 2.430 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 32.290 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.141 10727 Z= 0.556 Angle : 1.307 27.532 14513 Z= 0.782 Chirality : 0.060 0.477 1630 Planarity : 0.007 0.140 1865 Dihedral : 10.622 79.916 4023 Min Nonbonded Distance : 1.301 Molprobity Statistics. All-atom Clashscore : 55.14 Ramachandran Plot: Outliers : 1.07 % Allowed : 16.14 % Favored : 82.79 % Rotamer: Outliers : 0.17 % Allowed : 0.68 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.48 % 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: -5.50 (0.17), residues: 1307 helix: -4.49 (0.12), residues: 424 sheet: -3.01 (0.53), residues: 65 loop : -3.40 (0.18), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP A 76 HIS 0.012 0.003 HIS A 88 PHE 0.031 0.004 PHE A1154 TYR 0.055 0.003 TYR A 950 ARG 0.018 0.001 ARG A 162 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 380 time to evaluate : 1.365 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: A 147 LYS cc_start: 0.9298 (mttt) cc_final: 0.8991 (mtpt) REVERT: A 220 TRP cc_start: 0.8741 (m100) cc_final: 0.8461 (m100) REVERT: A 418 HIS cc_start: 0.8442 (m-70) cc_final: 0.8143 (m-70) REVERT: A 454 THR cc_start: 0.8189 (p) cc_final: 0.6872 (p) REVERT: A 548 PHE cc_start: 0.8310 (m-80) cc_final: 0.7993 (m-10) REVERT: A 967 ASP cc_start: 0.9120 (m-30) cc_final: 0.8538 (m-30) REVERT: A 1063 LEU cc_start: 0.8598 (tp) cc_final: 0.8308 (tp) REVERT: A 1123 ARG cc_start: 0.7548 (mtt180) cc_final: 0.6558 (ptp90) REVERT: A 1223 THR cc_start: 0.9079 (m) cc_final: 0.8615 (m) REVERT: A 1226 LYS cc_start: 0.9434 (mttt) cc_final: 0.9058 (mmtm) outliers start: 2 outliers final: 1 residues processed: 380 average time/residue: 0.3060 time to fit residues: 151.5343 Evaluate side-chains 239 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 238 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.9980 chunk 98 optimal weight: 6.9990 chunk 54 optimal weight: 0.2980 chunk 33 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN A 88 HIS A 206 ASN ** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 GLN A 444 HIS A 499 GLN ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 663 GLN A 778 GLN ** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1097 ASN ** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1236 ASN A1261 GLN A1322 ASN ** A1375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 10727 Z= 0.271 Angle : 0.900 12.818 14513 Z= 0.461 Chirality : 0.051 0.335 1630 Planarity : 0.006 0.054 1865 Dihedral : 10.102 79.196 1446 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 24.74 Ramachandran Plot: Outliers : 0.54 % Allowed : 11.40 % Favored : 88.06 % Rotamer: Outliers : 0.09 % Allowed : 3.49 % Favored : 96.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.08 % 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: -3.80 (0.20), residues: 1307 helix: -2.43 (0.20), residues: 468 sheet: -3.03 (0.48), residues: 80 loop : -2.59 (0.21), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 214 HIS 0.027 0.002 HIS A 956 PHE 0.018 0.002 PHE A1291 TYR 0.050 0.003 TYR A 950 ARG 0.012 0.001 ARG A1358 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 322 time to evaluate : 1.467 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: A 53 PHE cc_start: 0.7100 (m-10) cc_final: 0.6693 (m-10) REVERT: A 208 GLU cc_start: 0.8479 (tt0) cc_final: 0.8183 (tt0) REVERT: A 552 ASP cc_start: 0.5737 (t0) cc_final: 0.5446 (m-30) REVERT: A 553 TYR cc_start: 0.6833 (p90) cc_final: 0.6337 (p90) REVERT: A 635 LEU cc_start: 0.5542 (OUTLIER) cc_final: 0.5297 (pp) REVERT: A 749 GLN cc_start: 0.9149 (tt0) cc_final: 0.8748 (tp40) REVERT: A 795 TYR cc_start: 0.8748 (m-10) cc_final: 0.8254 (m-10) REVERT: A 870 ILE cc_start: 0.8407 (mm) cc_final: 0.8101 (mm) REVERT: A 894 LEU cc_start: 0.8843 (mt) cc_final: 0.8234 (mp) REVERT: A 941 LEU cc_start: 0.8723 (pt) cc_final: 0.8238 (pp) REVERT: A 967 ASP cc_start: 0.9082 (m-30) cc_final: 0.8713 (m-30) REVERT: A 1239 GLU cc_start: 0.7983 (pt0) cc_final: 0.7255 (pt0) REVERT: A 1339 GLN cc_start: 0.7756 (mt0) cc_final: 0.7420 (mt0) REVERT: A 1389 ILE cc_start: 0.5632 (mt) cc_final: 0.5081 (mt) REVERT: C 463 VAL cc_start: 0.9365 (t) cc_final: 0.9082 (t) outliers start: 1 outliers final: 0 residues processed: 323 average time/residue: 0.2876 time to fit residues: 122.6832 Evaluate side-chains 221 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 220 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 9.9990 chunk 36 optimal weight: 0.2980 chunk 98 optimal weight: 9.9990 chunk 80 optimal weight: 0.9990 chunk 32 optimal weight: 0.0570 chunk 118 optimal weight: 0.9990 chunk 127 optimal weight: 0.9990 chunk 105 optimal weight: 0.0020 chunk 117 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 overall best weight: 0.4710 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 206 ASN ** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 HIS A 655 ASN A 687 GLN A 778 GLN ** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 ASN A1097 ASN ** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1271 HIS ** A1383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.5219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10727 Z= 0.223 Angle : 0.809 12.268 14513 Z= 0.406 Chirality : 0.047 0.234 1630 Planarity : 0.009 0.314 1865 Dihedral : 9.597 80.312 1446 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 21.45 Ramachandran Plot: Outliers : 0.54 % Allowed : 10.56 % Favored : 88.91 % Rotamer: Outliers : 0.17 % Allowed : 3.75 % Favored : 96.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.08 % 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: -3.06 (0.22), residues: 1307 helix: -1.58 (0.21), residues: 474 sheet: -2.73 (0.45), residues: 98 loop : -2.29 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 990 HIS 0.011 0.001 HIS A 582 PHE 0.018 0.002 PHE A 954 TYR 0.036 0.002 TYR A 950 ARG 0.009 0.001 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 293 time to evaluate : 1.329 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: A 49 MET cc_start: 0.8659 (ptp) cc_final: 0.8299 (mpp) REVERT: A 68 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8180 (mm-30) REVERT: A 458 VAL cc_start: 0.9222 (t) cc_final: 0.8992 (t) REVERT: A 552 ASP cc_start: 0.5852 (t0) cc_final: 0.5087 (m-30) REVERT: A 635 LEU cc_start: 0.5112 (pp) cc_final: 0.4349 (pp) REVERT: A 787 ASN cc_start: 0.8914 (m-40) cc_final: 0.8707 (m-40) REVERT: A 870 ILE cc_start: 0.8318 (mm) cc_final: 0.7992 (mm) REVERT: A 941 LEU cc_start: 0.8615 (pt) cc_final: 0.8116 (pp) REVERT: A 967 ASP cc_start: 0.9125 (m-30) cc_final: 0.8731 (m-30) REVERT: A 1002 LEU cc_start: 0.8932 (tp) cc_final: 0.8721 (tt) REVERT: C 463 VAL cc_start: 0.9276 (t) cc_final: 0.8934 (t) outliers start: 2 outliers final: 0 residues processed: 295 average time/residue: 0.2647 time to fit residues: 104.6077 Evaluate side-chains 211 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 0.0870 chunk 88 optimal weight: 9.9990 chunk 61 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 125 optimal weight: 0.0770 chunk 62 optimal weight: 4.9990 chunk 112 optimal weight: 20.0000 chunk 33 optimal weight: 0.6980 overall best weight: 0.5116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 ASN ** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 778 GLN A 843 GLN ** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1296 ASN ** A1383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.5946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10727 Z= 0.202 Angle : 0.782 11.797 14513 Z= 0.387 Chirality : 0.047 0.256 1630 Planarity : 0.005 0.112 1865 Dihedral : 9.140 75.092 1446 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 21.16 Ramachandran Plot: Outliers : 0.54 % Allowed : 10.94 % Favored : 88.52 % Rotamer: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % 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: -2.91 (0.22), residues: 1307 helix: -1.24 (0.22), residues: 492 sheet: -2.86 (0.44), residues: 113 loop : -2.31 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 841 HIS 0.007 0.001 HIS A 582 PHE 0.023 0.002 PHE A 954 TYR 0.035 0.002 TYR A 950 ARG 0.006 0.001 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 285 time to evaluate : 1.174 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: A 44 LYS cc_start: 0.8260 (mttt) cc_final: 0.7863 (mmmt) REVERT: A 68 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8314 (mm-30) REVERT: A 239 TYR cc_start: 0.8641 (m-80) cc_final: 0.8248 (m-80) REVERT: A 443 LYS cc_start: 0.8701 (ttpt) cc_final: 0.8335 (tmtt) REVERT: A 497 ARG cc_start: 0.5983 (ptt180) cc_final: 0.4804 (tpt170) REVERT: A 552 ASP cc_start: 0.5969 (t0) cc_final: 0.4945 (m-30) REVERT: A 628 TYR cc_start: 0.8038 (m-10) cc_final: 0.7683 (m-10) REVERT: A 635 LEU cc_start: 0.5224 (pp) cc_final: 0.4255 (pp) REVERT: A 870 ILE cc_start: 0.8265 (mm) cc_final: 0.7920 (mm) REVERT: A 887 GLN cc_start: 0.7792 (mm-40) cc_final: 0.7568 (mm-40) REVERT: A 941 LEU cc_start: 0.8617 (pt) cc_final: 0.8081 (pp) REVERT: A 967 ASP cc_start: 0.9061 (m-30) cc_final: 0.8806 (m-30) REVERT: A 1041 LEU cc_start: 0.8436 (tt) cc_final: 0.8221 (tt) REVERT: A 1092 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8155 (pp20) REVERT: A 1239 GLU cc_start: 0.7445 (pm20) cc_final: 0.6548 (pm20) REVERT: A 1339 GLN cc_start: 0.7595 (mt0) cc_final: 0.7084 (mt0) REVERT: A 1389 ILE cc_start: 0.6137 (mt) cc_final: 0.5813 (mt) REVERT: C 463 VAL cc_start: 0.9253 (t) cc_final: 0.8901 (t) REVERT: C 470 GLN cc_start: 0.8663 (mt0) cc_final: 0.8351 (mt0) REVERT: C 488 GLN cc_start: 0.8685 (pp30) cc_final: 0.8263 (pp30) outliers start: 0 outliers final: 0 residues processed: 285 average time/residue: 0.2925 time to fit residues: 113.3801 Evaluate side-chains 216 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 9.9990 chunk 71 optimal weight: 0.7980 chunk 1 optimal weight: 10.0000 chunk 93 optimal weight: 0.9990 chunk 51 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 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 33 GLN ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 174 HIS A 206 ASN ** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 HIS ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 GLN ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 778 GLN ** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 956 HIS ** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1348 GLN ** A1383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 GLN C 474 GLN ** C 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.6165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10727 Z= 0.257 Angle : 0.771 11.679 14513 Z= 0.382 Chirality : 0.046 0.322 1630 Planarity : 0.005 0.062 1865 Dihedral : 8.951 74.206 1446 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 23.59 Ramachandran Plot: Outliers : 0.54 % Allowed : 11.71 % Favored : 87.76 % Rotamer: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.08 % 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: -2.66 (0.22), residues: 1307 helix: -1.06 (0.22), residues: 493 sheet: -2.68 (0.47), residues: 103 loop : -2.18 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 214 HIS 0.006 0.001 HIS A 418 PHE 0.038 0.002 PHE A 954 TYR 0.038 0.002 TYR A 950 ARG 0.006 0.001 ARG A1184 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 1.482 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: A 44 LYS cc_start: 0.8383 (mttt) cc_final: 0.7988 (mmtt) REVERT: A 49 MET cc_start: 0.8554 (mpp) cc_final: 0.8119 (mpp) REVERT: A 68 GLU cc_start: 0.8760 (mm-30) cc_final: 0.8462 (mm-30) REVERT: A 80 GLU cc_start: 0.8214 (tt0) cc_final: 0.7974 (tp30) REVERT: A 216 GLU cc_start: 0.9197 (mp0) cc_final: 0.8991 (mp0) REVERT: A 236 ILE cc_start: 0.6963 (pt) cc_final: 0.6748 (pt) REVERT: A 443 LYS cc_start: 0.8786 (ttpt) cc_final: 0.8311 (tmtt) REVERT: A 635 LEU cc_start: 0.5535 (pp) cc_final: 0.5016 (pp) REVERT: A 825 MET cc_start: 0.6758 (mtt) cc_final: 0.5824 (mtt) REVERT: A 941 LEU cc_start: 0.8680 (pt) cc_final: 0.8077 (pp) REVERT: A 967 ASP cc_start: 0.9081 (m-30) cc_final: 0.8861 (m-30) REVERT: A 1092 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8318 (pp20) REVERT: A 1123 ARG cc_start: 0.6987 (mtt180) cc_final: 0.6430 (ptp90) REVERT: A 1277 ASP cc_start: 0.7802 (t0) cc_final: 0.7584 (t0) REVERT: A 1281 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7688 (mt-10) REVERT: A 1339 GLN cc_start: 0.7662 (mt0) cc_final: 0.7040 (mt0) REVERT: C 463 VAL cc_start: 0.9276 (t) cc_final: 0.8959 (t) REVERT: C 470 GLN cc_start: 0.8771 (mt0) cc_final: 0.8365 (mt0) REVERT: C 488 GLN cc_start: 0.8713 (pp30) cc_final: 0.8354 (pp30) outliers start: 0 outliers final: 0 residues processed: 259 average time/residue: 0.2497 time to fit residues: 88.9780 Evaluate side-chains 189 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 6.9990 chunk 113 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 73 optimal weight: 0.0570 chunk 31 optimal weight: 0.9990 chunk 125 optimal weight: 0.7980 chunk 104 optimal weight: 6.9990 chunk 58 optimal weight: 0.8980 chunk 10 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 overall best weight: 1.3502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 ASN ** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 HIS ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 778 GLN ** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1348 GLN ** A1383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.6461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10727 Z= 0.214 Angle : 0.765 11.909 14513 Z= 0.375 Chirality : 0.046 0.370 1630 Planarity : 0.005 0.106 1865 Dihedral : 8.800 74.437 1446 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 22.07 Ramachandran Plot: Outliers : 0.54 % Allowed : 11.55 % Favored : 87.91 % Rotamer: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.08 % 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: -2.63 (0.22), residues: 1307 helix: -0.93 (0.23), residues: 500 sheet: -2.83 (0.43), residues: 120 loop : -2.18 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 214 HIS 0.006 0.001 HIS A 418 PHE 0.042 0.002 PHE A1314 TYR 0.037 0.002 TYR A 950 ARG 0.017 0.001 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 1.305 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: A 44 LYS cc_start: 0.8468 (mttt) cc_final: 0.8194 (mmtt) REVERT: A 49 MET cc_start: 0.8448 (mpp) cc_final: 0.8031 (mpp) REVERT: A 68 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8187 (mm-30) REVERT: A 80 GLU cc_start: 0.8117 (tt0) cc_final: 0.7868 (tp30) REVERT: A 417 ARG cc_start: 0.8058 (mtt180) cc_final: 0.7809 (mtt180) REVERT: A 635 LEU cc_start: 0.5271 (pp) cc_final: 0.4691 (pp) REVERT: A 825 MET cc_start: 0.6636 (mtt) cc_final: 0.5683 (mtt) REVERT: A 850 LEU cc_start: 0.9418 (tt) cc_final: 0.9119 (tp) REVERT: A 941 LEU cc_start: 0.8652 (pt) cc_final: 0.8023 (pp) REVERT: A 1092 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8267 (pp20) REVERT: A 1277 ASP cc_start: 0.7897 (t0) cc_final: 0.7582 (t0) REVERT: A 1281 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7559 (mt-10) REVERT: A 1314 PHE cc_start: 0.8522 (m-80) cc_final: 0.8015 (m-80) REVERT: A 1339 GLN cc_start: 0.7592 (mt0) cc_final: 0.7043 (mt0) REVERT: C 435 LYS cc_start: 0.8283 (tmmt) cc_final: 0.7755 (tttt) REVERT: C 463 VAL cc_start: 0.9288 (t) cc_final: 0.8890 (t) REVERT: C 470 GLN cc_start: 0.8711 (mt0) cc_final: 0.8249 (mt0) REVERT: C 488 GLN cc_start: 0.8686 (pp30) cc_final: 0.8420 (pp30) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.2536 time to fit residues: 91.9471 Evaluate side-chains 198 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 71 optimal weight: 10.0000 chunk 91 optimal weight: 0.0040 chunk 105 optimal weight: 0.0270 chunk 70 optimal weight: 1.9990 chunk 125 optimal weight: 10.0000 chunk 78 optimal weight: 0.9980 chunk 76 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.0054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN ** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 HIS ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 778 GLN ** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.6753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10727 Z= 0.199 Angle : 0.749 11.287 14513 Z= 0.366 Chirality : 0.046 0.292 1630 Planarity : 0.005 0.054 1865 Dihedral : 8.630 72.262 1446 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 21.49 Ramachandran Plot: Outliers : 0.54 % Allowed : 11.63 % Favored : 87.83 % Rotamer: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % 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: -2.57 (0.23), residues: 1307 helix: -0.86 (0.23), residues: 501 sheet: -2.64 (0.43), residues: 124 loop : -2.20 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 214 HIS 0.007 0.001 HIS A1271 PHE 0.030 0.001 PHE A1314 TYR 0.039 0.002 TYR A 950 ARG 0.008 0.001 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 258 time to evaluate : 1.305 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: A 44 LYS cc_start: 0.8451 (mttt) cc_final: 0.8225 (mmtt) REVERT: A 49 MET cc_start: 0.8427 (mpp) cc_final: 0.8019 (mpp) REVERT: A 68 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8445 (mm-30) REVERT: A 80 GLU cc_start: 0.8132 (tt0) cc_final: 0.7889 (tp30) REVERT: A 236 ILE cc_start: 0.6875 (pt) cc_final: 0.6637 (pt) REVERT: A 410 ASN cc_start: 0.9142 (t0) cc_final: 0.8725 (t0) REVERT: A 635 LEU cc_start: 0.5329 (pp) cc_final: 0.4560 (pp) REVERT: A 677 LEU cc_start: 0.9135 (tt) cc_final: 0.8897 (tt) REVERT: A 768 ASP cc_start: 0.8476 (t0) cc_final: 0.8196 (t0) REVERT: A 825 MET cc_start: 0.6532 (mtt) cc_final: 0.5548 (mtt) REVERT: A 850 LEU cc_start: 0.9458 (tt) cc_final: 0.9161 (tp) REVERT: A 870 ILE cc_start: 0.8086 (mm) cc_final: 0.7769 (mm) REVERT: A 941 LEU cc_start: 0.8734 (pt) cc_final: 0.8172 (pp) REVERT: A 967 ASP cc_start: 0.9125 (m-30) cc_final: 0.8848 (m-30) REVERT: A 1092 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8174 (pp20) REVERT: A 1281 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7488 (mt-10) REVERT: A 1314 PHE cc_start: 0.8590 (m-80) cc_final: 0.7721 (m-80) REVERT: A 1339 GLN cc_start: 0.7547 (mt0) cc_final: 0.7024 (mt0) REVERT: A 1356 LEU cc_start: 0.8059 (tt) cc_final: 0.7388 (pt) REVERT: C 435 LYS cc_start: 0.8291 (tmmt) cc_final: 0.7869 (ttpp) REVERT: C 463 VAL cc_start: 0.9288 (t) cc_final: 0.8844 (t) REVERT: C 470 GLN cc_start: 0.8729 (mt0) cc_final: 0.8264 (mt0) outliers start: 0 outliers final: 0 residues processed: 258 average time/residue: 0.2463 time to fit residues: 87.6099 Evaluate side-chains 199 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 37 optimal weight: 8.9990 chunk 24 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 98 optimal weight: 8.9990 chunk 113 optimal weight: 8.9990 chunk 120 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN ** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 687 GLN ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 778 GLN ** A 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1153 ASN ** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1337 GLN A1348 GLN ** A1375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.6771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10727 Z= 0.308 Angle : 0.817 11.944 14513 Z= 0.406 Chirality : 0.047 0.181 1630 Planarity : 0.005 0.056 1865 Dihedral : 8.797 74.354 1446 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 27.21 Ramachandran Plot: Outliers : 0.54 % Allowed : 12.47 % Favored : 86.99 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.08 % 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: -2.71 (0.22), residues: 1307 helix: -0.88 (0.22), residues: 503 sheet: -2.94 (0.40), residues: 127 loop : -2.32 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 169 HIS 0.010 0.001 HIS A 418 PHE 0.043 0.002 PHE A 954 TYR 0.023 0.002 TYR A 950 ARG 0.013 0.001 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 249 time to evaluate : 1.285 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: A 49 MET cc_start: 0.8281 (mpp) cc_final: 0.7995 (mpp) REVERT: A 80 GLU cc_start: 0.8137 (tt0) cc_final: 0.7906 (tp30) REVERT: A 236 ILE cc_start: 0.7041 (pt) cc_final: 0.6749 (pt) REVERT: A 537 SER cc_start: 0.8798 (m) cc_final: 0.8479 (p) REVERT: A 635 LEU cc_start: 0.5793 (pp) cc_final: 0.5446 (pp) REVERT: A 749 GLN cc_start: 0.8498 (tm-30) cc_final: 0.8008 (tm-30) REVERT: A 825 MET cc_start: 0.6443 (mtt) cc_final: 0.6047 (mtt) REVERT: A 850 LEU cc_start: 0.9586 (tt) cc_final: 0.9336 (tp) REVERT: A 870 ILE cc_start: 0.7971 (mm) cc_final: 0.7652 (mm) REVERT: A 941 LEU cc_start: 0.8942 (pt) cc_final: 0.8452 (pp) REVERT: A 967 ASP cc_start: 0.9131 (m-30) cc_final: 0.8839 (m-30) REVERT: A 1277 ASP cc_start: 0.7738 (t0) cc_final: 0.7367 (t0) REVERT: A 1281 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7643 (mt-10) REVERT: A 1314 PHE cc_start: 0.8612 (m-80) cc_final: 0.7985 (m-80) REVERT: A 1339 GLN cc_start: 0.7759 (mt0) cc_final: 0.7115 (mt0) REVERT: A 1356 LEU cc_start: 0.8096 (tt) cc_final: 0.7371 (pt) REVERT: C 435 LYS cc_start: 0.8381 (tmmt) cc_final: 0.7906 (ttpp) REVERT: C 463 VAL cc_start: 0.9325 (t) cc_final: 0.8927 (t) REVERT: C 470 GLN cc_start: 0.8828 (mt0) cc_final: 0.8386 (mt0) REVERT: C 473 GLN cc_start: 0.9087 (mp10) cc_final: 0.8859 (mp10) outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.2540 time to fit residues: 86.1298 Evaluate side-chains 185 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 35 optimal weight: 0.2980 chunk 105 optimal weight: 9.9990 chunk 110 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 123 optimal weight: 10.0000 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 GLN ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 778 GLN ** A 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1153 ASN ** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1348 GLN ** A1375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 GLN ** C 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.7121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10727 Z= 0.198 Angle : 0.778 10.759 14513 Z= 0.381 Chirality : 0.046 0.179 1630 Planarity : 0.005 0.056 1865 Dihedral : 8.598 72.951 1446 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 21.26 Ramachandran Plot: Outliers : 0.54 % Allowed : 11.78 % Favored : 87.68 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % 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: -2.62 (0.22), residues: 1307 helix: -0.80 (0.22), residues: 495 sheet: -2.63 (0.42), residues: 122 loop : -2.31 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 220 HIS 0.009 0.001 HIS A1303 PHE 0.032 0.002 PHE A 938 TYR 0.038 0.002 TYR A 950 ARG 0.009 0.001 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 253 time to evaluate : 1.276 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: A 236 ILE cc_start: 0.6644 (pt) cc_final: 0.6395 (pt) REVERT: A 455 ILE cc_start: 0.8118 (mt) cc_final: 0.7891 (mt) REVERT: A 635 LEU cc_start: 0.5292 (pp) cc_final: 0.4540 (pp) REVERT: A 749 GLN cc_start: 0.8409 (tm-30) cc_final: 0.8074 (tm-30) REVERT: A 825 MET cc_start: 0.6279 (mtt) cc_final: 0.6005 (mtt) REVERT: A 830 ASP cc_start: 0.8709 (p0) cc_final: 0.8504 (p0) REVERT: A 850 LEU cc_start: 0.9559 (tt) cc_final: 0.9295 (tp) REVERT: A 870 ILE cc_start: 0.8065 (mm) cc_final: 0.7721 (mm) REVERT: A 941 LEU cc_start: 0.8826 (pt) cc_final: 0.8292 (pp) REVERT: A 1131 MET cc_start: 0.7916 (tmm) cc_final: 0.7708 (tmm) REVERT: A 1277 ASP cc_start: 0.7939 (t0) cc_final: 0.7682 (t0) REVERT: A 1281 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7469 (mt-10) REVERT: A 1314 PHE cc_start: 0.8495 (m-80) cc_final: 0.8190 (m-10) REVERT: A 1335 ARG cc_start: 0.6618 (mtp180) cc_final: 0.6265 (mtp180) REVERT: C 435 LYS cc_start: 0.8322 (tmmt) cc_final: 0.7848 (ttpp) REVERT: C 463 VAL cc_start: 0.9286 (t) cc_final: 0.8812 (t) REVERT: C 470 GLN cc_start: 0.8865 (mt0) cc_final: 0.8314 (mt0) REVERT: C 473 GLN cc_start: 0.9095 (mp10) cc_final: 0.8741 (mp10) outliers start: 0 outliers final: 0 residues processed: 253 average time/residue: 0.2546 time to fit residues: 88.4006 Evaluate side-chains 191 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 85 optimal weight: 0.3980 chunk 129 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 63 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 109 optimal weight: 0.0070 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 778 GLN ** A 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1348 GLN ** A1375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 489 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.7324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10727 Z= 0.207 Angle : 0.792 15.121 14513 Z= 0.391 Chirality : 0.048 0.511 1630 Planarity : 0.005 0.080 1865 Dihedral : 8.504 71.612 1446 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 22.30 Ramachandran Plot: Outliers : 0.46 % Allowed : 12.09 % Favored : 87.45 % 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 : 1.96 % Twisted General : 0.08 % 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: -2.59 (0.22), residues: 1307 helix: -0.76 (0.23), residues: 491 sheet: -2.60 (0.46), residues: 107 loop : -2.32 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 169 HIS 0.011 0.001 HIS A 418 PHE 0.025 0.002 PHE A1314 TYR 0.051 0.002 TYR A 950 ARG 0.022 0.001 ARG A 417 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 246 time to evaluate : 1.361 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: A 236 ILE cc_start: 0.6658 (pt) cc_final: 0.6395 (pt) REVERT: A 677 LEU cc_start: 0.9174 (tt) cc_final: 0.8971 (tt) REVERT: A 749 GLN cc_start: 0.8298 (tm-30) cc_final: 0.7962 (tm-30) REVERT: A 825 MET cc_start: 0.6095 (mtt) cc_final: 0.5460 (mtt) REVERT: A 850 LEU cc_start: 0.9580 (tt) cc_final: 0.9255 (mt) REVERT: A 870 ILE cc_start: 0.8042 (mm) cc_final: 0.7710 (mm) REVERT: A 941 LEU cc_start: 0.8811 (pt) cc_final: 0.8299 (pp) REVERT: A 967 ASP cc_start: 0.9115 (m-30) cc_final: 0.8904 (m-30) REVERT: A 1277 ASP cc_start: 0.8070 (t0) cc_final: 0.7769 (t0) REVERT: A 1281 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7409 (mt-10) REVERT: A 1314 PHE cc_start: 0.8489 (m-80) cc_final: 0.7607 (m-80) REVERT: A 1335 ARG cc_start: 0.6429 (mtp180) cc_final: 0.5919 (mtp180) REVERT: A 1339 GLN cc_start: 0.7555 (mt0) cc_final: 0.7098 (mt0) REVERT: C 435 LYS cc_start: 0.8312 (tmmt) cc_final: 0.7893 (tmtt) REVERT: C 463 VAL cc_start: 0.9389 (t) cc_final: 0.8911 (t) REVERT: C 470 GLN cc_start: 0.8901 (mt0) cc_final: 0.8338 (mt0) REVERT: C 473 GLN cc_start: 0.9109 (mp10) cc_final: 0.8784 (mp10) outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.2627 time to fit residues: 88.6081 Evaluate side-chains 191 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 0.8980 chunk 95 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 13 optimal weight: 0.0770 chunk 19 optimal weight: 2.9990 chunk 90 optimal weight: 0.3980 chunk 5 optimal weight: 0.8980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 GLN A 463 ASN ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 922 ASN ** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1312 ASN A1315 GLN ** A1339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 ASN C 474 GLN C 489 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.084849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.071004 restraints weight = 45187.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.073216 restraints weight = 30192.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.074834 restraints weight = 21990.667| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.7614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10727 Z= 0.187 Angle : 0.754 10.484 14513 Z= 0.371 Chirality : 0.045 0.222 1630 Planarity : 0.004 0.055 1865 Dihedral : 8.306 72.631 1446 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 19.83 Ramachandran Plot: Outliers : 0.54 % Allowed : 11.48 % Favored : 87.99 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % 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: -2.59 (0.22), residues: 1307 helix: -0.72 (0.23), residues: 505 sheet: -2.66 (0.48), residues: 97 loop : -2.40 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 76 HIS 0.008 0.001 HIS A 418 PHE 0.025 0.001 PHE A1314 TYR 0.031 0.001 TYR A 950 ARG 0.008 0.001 ARG A 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2731.30 seconds wall clock time: 50 minutes 14.01 seconds (3014.01 seconds total)