Starting phenix.real_space_refine on Sat Dec 9 08:50:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yud_6845/12_2023/5yud_6845_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yud_6845/12_2023/5yud_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_6845/12_2023/5yud_6845.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yud_6845/12_2023/5yud_6845.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yud_6845/12_2023/5yud_6845_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yud_6845/12_2023/5yud_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 5.70, per 1000 atoms: 0.54 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: 4.56 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: 2.77 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: 3.16 Time building geometry restraints manager: 4.84 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: 0.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 2.360 Check model and map are aligned: 0.160 Set scattering table: 0.090 Process input model: 31.060 Find NCS groups from input model: 0.270 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: 37.430 ------------------------------------------------------------------------------- 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 : 1.345 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 outliers start: 2 outliers final: 1 residues processed: 380 average time/residue: 0.3116 time to fit residues: 154.7482 Evaluate side-chains 234 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 233 time to evaluate : 1.306 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1485 time to fit residues: 2.0250 ------------------------------------------------------------------------------- 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: 0.7485 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 10727 Z= 0.271 Angle : 0.903 12.806 14513 Z= 0.461 Chirality : 0.051 0.348 1630 Planarity : 0.006 0.054 1865 Dihedral : 10.161 80.398 1446 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 25.36 Ramachandran Plot: Outliers : 0.54 % Allowed : 11.17 % Favored : 88.29 % 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: -3.83 (0.20), residues: 1307 helix: -2.45 (0.20), residues: 468 sheet: -3.05 (0.47), residues: 81 loop : -2.62 (0.21), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 220 HIS 0.009 0.002 HIS A 956 PHE 0.018 0.002 PHE A1291 TYR 0.051 0.003 TYR A 950 ARG 0.017 0.001 ARG A 765 *********************** 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 : 1.368 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 outliers start: 1 outliers final: 0 residues processed: 323 average time/residue: 0.2837 time to fit residues: 121.8996 Evaluate side-chains 212 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 1.328 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7741 ------------------------------------------------------------------------------- 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: 7.9990 chunk 36 optimal weight: 0.1980 chunk 98 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 32 optimal weight: 0.0070 chunk 118 optimal weight: 5.9990 chunk 127 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 117 optimal weight: 0.8980 chunk 40 optimal weight: 8.9990 chunk 94 optimal weight: 0.9980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 HIS ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 ASN A 687 GLN A 778 GLN A 843 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: 0.7464 moved from start: 0.5194 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= 0.215 Angle : 0.808 12.601 14513 Z= 0.408 Chirality : 0.047 0.233 1630 Planarity : 0.005 0.058 1865 Dihedral : 9.447 73.438 1446 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 21.73 Ramachandran Plot: Outliers : 0.54 % Allowed : 10.86 % Favored : 88.60 % 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: -3.12 (0.22), residues: 1307 helix: -1.63 (0.21), residues: 476 sheet: -2.83 (0.44), residues: 98 loop : -2.31 (0.23), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 990 HIS 0.009 0.001 HIS A 582 PHE 0.022 0.002 PHE A 954 TYR 0.034 0.002 TYR A 950 ARG 0.008 0.001 ARG A 92 *********************** 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 293 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 291 time to evaluate : 1.316 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 outliers start: 2 outliers final: 1 residues processed: 293 average time/residue: 0.2705 time to fit residues: 107.1245 Evaluate side-chains 202 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 201 time to evaluate : 1.229 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1348 time to fit residues: 1.8893 ------------------------------------------------------------------------------- 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: 2.9990 chunk 88 optimal weight: 0.0670 chunk 61 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 56 optimal weight: 8.9990 chunk 79 optimal weight: 7.9990 chunk 118 optimal weight: 3.9990 chunk 125 optimal weight: 0.0060 chunk 62 optimal weight: 1.9990 chunk 112 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.6736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 HIS ** A 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 778 GLN A 787 ASN ** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1296 ASN ** A1375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1383 GLN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.5883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10727 Z= 0.204 Angle : 0.792 12.185 14513 Z= 0.394 Chirality : 0.047 0.220 1630 Planarity : 0.006 0.144 1865 Dihedral : 9.225 74.445 1446 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 21.59 Ramachandran Plot: Outliers : 0.54 % Allowed : 11.02 % Favored : 88.45 % Rotamer: Outliers : 0.09 % Allowed : 3.15 % 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: -3.03 (0.22), residues: 1307 helix: -1.36 (0.22), residues: 486 sheet: -2.83 (0.44), residues: 113 loop : -2.38 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 220 HIS 0.009 0.001 HIS A 582 PHE 0.021 0.002 PHE A 954 TYR 0.039 0.002 TYR A 950 ARG 0.007 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 280 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 279 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 279 average time/residue: 0.2631 time to fit residues: 100.6450 Evaluate side-chains 199 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 1.391 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7789 ------------------------------------------------------------------------------- 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: 10.0000 chunk 71 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 93 optimal weight: 0.9980 chunk 51 optimal weight: 9.9990 chunk 107 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 64 optimal weight: 3.9990 chunk 112 optimal weight: 9.9990 chunk 31 optimal weight: 8.9990 overall best weight: 3.9786 ------------------------------------------------------------------------------- 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 ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 687 GLN A 778 GLN ** A 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1130 HIS A1153 ASN ** A1212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1337 GLN ** A1348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 GLN ** C 465 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.5919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 10727 Z= 0.373 Angle : 0.876 12.090 14513 Z= 0.439 Chirality : 0.049 0.216 1630 Planarity : 0.006 0.077 1865 Dihedral : 9.200 61.173 1446 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 31.79 Ramachandran Plot: Outliers : 0.54 % Allowed : 12.09 % Favored : 87.38 % Rotamer: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % 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: -3.03 (0.22), residues: 1307 helix: -1.19 (0.22), residues: 499 sheet: -2.93 (0.43), residues: 103 loop : -2.53 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A1391 HIS 0.011 0.002 HIS A 582 PHE 0.028 0.002 PHE A1314 TYR 0.028 0.003 TYR A 950 ARG 0.034 0.001 ARG A1335 *********************** 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 239 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 1.158 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 outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.2669 time to fit residues: 88.4957 Evaluate side-chains 180 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 1.240 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7903 ------------------------------------------------------------------------------- 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: 0.5980 chunk 113 optimal weight: 5.9990 chunk 24 optimal weight: 0.5980 chunk 73 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 125 optimal weight: 0.0070 chunk 104 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 overall best weight: 0.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 HIS ** 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 778 GLN ** A 887 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** A1312 ASN A1315 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 474 GLN ** C 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.6471 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= 0.197 Angle : 0.780 11.402 14513 Z= 0.385 Chirality : 0.046 0.190 1630 Planarity : 0.005 0.058 1865 Dihedral : 8.881 66.319 1446 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 22.11 Ramachandran Plot: Outliers : 0.46 % Allowed : 11.55 % Favored : 87.99 % 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 : 0.08 % 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: -2.76 (0.22), residues: 1307 helix: -0.99 (0.22), residues: 489 sheet: -2.97 (0.42), residues: 113 loop : -2.29 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 214 HIS 0.011 0.001 HIS A 418 PHE 0.034 0.002 PHE A 629 TYR 0.019 0.002 TYR A 873 ARG 0.012 0.001 ARG A 417 *********************** 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 261 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 1.204 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 outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 0.2707 time to fit residues: 95.9534 Evaluate side-chains 201 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 1.304 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6275 ------------------------------------------------------------------------------- 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: 6.9990 chunk 14 optimal weight: 9.9990 chunk 71 optimal weight: 7.9990 chunk 91 optimal weight: 8.9990 chunk 105 optimal weight: 0.8980 chunk 70 optimal weight: 0.5980 chunk 125 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 57 optimal weight: 0.2980 chunk 77 optimal weight: 0.0270 overall best weight: 0.7640 ------------------------------------------------------------------------------- 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 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 778 GLN ** A 887 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1099 HIS ** 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 465 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.6796 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= 0.195 Angle : 0.760 11.651 14513 Z= 0.373 Chirality : 0.046 0.240 1630 Planarity : 0.005 0.053 1865 Dihedral : 8.662 65.795 1446 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 22.30 Ramachandran Plot: Outliers : 0.61 % Allowed : 11.63 % Favored : 87.76 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % 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: -0.85 (0.23), residues: 489 sheet: -2.63 (0.43), residues: 117 loop : -2.23 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 220 HIS 0.005 0.001 HIS A 582 PHE 0.030 0.002 PHE A 954 TYR 0.022 0.002 TYR A 873 ARG 0.005 0.001 ARG A 417 *********************** 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 254 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 1.234 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 outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.2638 time to fit residues: 91.9444 Evaluate side-chains 200 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 1.255 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8285 ------------------------------------------------------------------------------- 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: 0.7980 chunk 74 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 24 optimal weight: 0.2980 chunk 79 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 61 optimal weight: 20.0000 chunk 11 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 chunk 113 optimal weight: 7.9990 chunk 120 optimal weight: 0.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 778 GLN ** A 887 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1315 GLN ** A1339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.6934 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= 0.271 Angle : 0.790 11.950 14513 Z= 0.397 Chirality : 0.047 0.220 1630 Planarity : 0.005 0.061 1865 Dihedral : 8.656 61.101 1446 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 27.07 Ramachandran Plot: Outliers : 0.61 % Allowed : 11.71 % Favored : 87.68 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % 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: -2.67 (0.22), residues: 1307 helix: -0.86 (0.22), residues: 502 sheet: -2.72 (0.45), residues: 112 loop : -2.34 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 76 HIS 0.008 0.002 HIS A 157 PHE 0.042 0.002 PHE A 954 TYR 0.035 0.002 TYR A 950 ARG 0.017 0.001 ARG A 417 *********************** 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 247 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 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: symmetry clash outliers start: 0 outliers final: 0 residues processed: 247 average time/residue: 0.2627 time to fit residues: 88.9991 Evaluate side-chains 179 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.248 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7070 ------------------------------------------------------------------------------- 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: 0.0870 chunk 116 optimal weight: 7.9990 chunk 120 optimal weight: 0.0050 chunk 70 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 91 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 76 optimal weight: 8.9990 chunk 123 optimal weight: 6.9990 overall best weight: 0.9574 ------------------------------------------------------------------------------- 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 778 GLN ** A 887 GLN ** 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** ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.7234 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= 0.213 Angle : 0.808 13.590 14513 Z= 0.397 Chirality : 0.047 0.304 1630 Planarity : 0.005 0.054 1865 Dihedral : 8.502 62.043 1446 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 23.16 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 : 0.08 % 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: -0.84 (0.23), residues: 489 sheet: -2.53 (0.45), residues: 107 loop : -2.33 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 487 HIS 0.016 0.002 HIS A1249 PHE 0.058 0.002 PHE A1390 TYR 0.048 0.002 TYR A 950 ARG 0.021 0.001 ARG A 417 *********************** 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 : 1.228 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 outliers start: 0 outliers final: 0 residues processed: 253 average time/residue: 0.2664 time to fit residues: 91.7057 Evaluate side-chains 188 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 1.308 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7527 ------------------------------------------------------------------------------- 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: 10.0000 chunk 58 optimal weight: 0.8980 chunk 85 optimal weight: 0.2980 chunk 129 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 103 optimal weight: 0.0040 chunk 10 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 109 optimal weight: 0.8980 overall best weight: 0.5592 ------------------------------------------------------------------------------- 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 ** A 418 HIS ** 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 663 GLN A 778 GLN ** A 887 GLN ** 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** A1236 ASN A1348 GLN ** A1375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1383 GLN ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.7552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10727 Z= 0.204 Angle : 0.818 12.053 14513 Z= 0.399 Chirality : 0.050 0.597 1630 Planarity : 0.005 0.070 1865 Dihedral : 8.333 59.894 1446 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 22.40 Ramachandran Plot: Outliers : 0.54 % Allowed : 11.02 % Favored : 88.45 % Rotamer: Outliers : 0.09 % Allowed : 0.43 % Favored : 99.49 % 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: -0.75 (0.23), residues: 493 sheet: -2.50 (0.46), residues: 107 loop : -2.36 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 220 HIS 0.011 0.001 HIS A 418 PHE 0.049 0.002 PHE A 954 TYR 0.048 0.002 TYR A 950 ARG 0.020 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 249 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 248 time to evaluate : 1.288 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 outliers start: 1 outliers final: 0 residues processed: 249 average time/residue: 0.2578 time to fit residues: 88.9077 Evaluate side-chains 185 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 1.293 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9040 ------------------------------------------------------------------------------- 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: 2.9990 chunk 95 optimal weight: 0.0670 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 overall best weight: 1.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 GLN A 418 HIS ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 749 GLN A 778 GLN ** A 887 GLN ** 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** A1236 ASN ** A1249 HIS ** 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 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.084184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.070799 restraints weight = 46318.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.072917 restraints weight = 30623.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.074452 restraints weight = 22297.532| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.7650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10727 Z= 0.216 Angle : 0.800 13.669 14513 Z= 0.391 Chirality : 0.047 0.283 1630 Planarity : 0.005 0.053 1865 Dihedral : 8.237 60.013 1446 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 22.59 Ramachandran Plot: Outliers : 0.54 % Allowed : 11.63 % Favored : 87.83 % 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 : 0.00 % 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: -2.73 (0.22), residues: 1307 helix: -0.83 (0.22), residues: 504 sheet: -2.62 (0.46), residues: 97 loop : -2.50 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP A 220 HIS 0.012 0.001 HIS A1249 PHE 0.035 0.002 PHE A 954 TYR 0.048 0.002 TYR A 950 ARG 0.012 0.001 ARG A 58 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2709.63 seconds wall clock time: 50 minutes 4.35 seconds (3004.35 seconds total)