Starting phenix.real_space_refine on Sun Apr 7 02:15:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wom_37692/04_2024/8wom_37692_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wom_37692/04_2024/8wom_37692.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wom_37692/04_2024/8wom_37692.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wom_37692/04_2024/8wom_37692.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wom_37692/04_2024/8wom_37692_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wom_37692/04_2024/8wom_37692_neut_updated.pdb" } resolution = 3.5 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= 0.006 sd= 0.096 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 38 5.16 5 C 5987 2.51 5 N 1583 2.21 5 O 1740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 9348 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1217, 9314 Classifications: {'peptide': 1217} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 30, 'TRANS': 1186} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'BLD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.38, per 1000 atoms: 0.58 Number of scatterers: 9348 At special positions: 0 Unit cell: (73.7, 106.7, 144.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 38 16.00 O 1740 8.00 N 1583 7.00 C 5987 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=0, symmetry=0 Time building additional restraints: 3.21 Conformation dependent library (CDL) restraints added in 1.8 seconds 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2228 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 63 helices and 5 sheets defined 38.9% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.67 Creating SS restraints... Processing helix chain 'A' and resid 37 through 40 No H-bonds generated for 'chain 'A' and resid 37 through 40' Processing helix chain 'A' and resid 47 through 50 No H-bonds generated for 'chain 'A' and resid 47 through 50' Processing helix chain 'A' and resid 52 through 70 removed outlier: 3.885A pdb=" N MET A 55 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Proline residue: A 56 - end of helix removed outlier: 4.202A pdb=" N PHE A 59 " --> pdb=" O PRO A 56 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N PHE A 62 " --> pdb=" O PHE A 59 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N MET A 65 " --> pdb=" O PHE A 62 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN A 67 " --> pdb=" O GLN A 64 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLY A 70 " --> pdb=" O ASN A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 101 removed outlier: 4.463A pdb=" N TYR A 86 " --> pdb=" O GLU A 82 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU A 88 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE A 90 " --> pdb=" O TYR A 86 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL A 96 " --> pdb=" O TYR A 92 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N PHE A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER A 100 " --> pdb=" O VAL A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 126 removed outlier: 3.841A pdb=" N GLU A 125 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 144 through 149 Processing helix chain 'A' and resid 151 through 159 removed outlier: 3.565A pdb=" N VAL A 155 " --> pdb=" O ASP A 151 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN A 156 " --> pdb=" O THR A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 175 removed outlier: 3.617A pdb=" N TYR A 169 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU A 170 " --> pdb=" O PHE A 166 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE A 173 " --> pdb=" O TYR A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 183 Processing helix chain 'A' and resid 191 through 208 removed outlier: 3.844A pdb=" N ILE A 195 " --> pdb=" O SER A 191 " (cutoff:3.500A) Proline residue: A 196 - end of helix removed outlier: 3.916A pdb=" N PHE A 200 " --> pdb=" O PRO A 196 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ALA A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR A 205 " --> pdb=" O ALA A 201 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ALA A 206 " --> pdb=" O GLY A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 220 removed outlier: 4.392A pdb=" N LYS A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU A 218 " --> pdb=" O SER A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 232 removed outlier: 4.670A pdb=" N ILE A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 237 No H-bonds generated for 'chain 'A' and resid 234 through 237' Processing helix chain 'A' and resid 255 through 262 removed outlier: 3.745A pdb=" N LYS A 259 " --> pdb=" O GLN A 255 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU A 260 " --> pdb=" O TYR A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 272 removed outlier: 4.290A pdb=" N GLY A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 279 No H-bonds generated for 'chain 'A' and resid 276 through 279' Processing helix chain 'A' and resid 283 through 293 removed outlier: 3.612A pdb=" N ALA A 290 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY A 291 " --> pdb=" O PHE A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 313 removed outlier: 3.697A pdb=" N PHE A 309 " --> pdb=" O PHE A 305 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA A 311 " --> pdb=" O ALA A 307 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE A 312 " --> pdb=" O ILE A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 318 No H-bonds generated for 'chain 'A' and resid 316 through 318' Processing helix chain 'A' and resid 327 through 338 removed outlier: 3.646A pdb=" N GLY A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS A 332 " --> pdb=" O PHE A 328 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU A 338 " --> pdb=" O ALA A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 413 removed outlier: 4.206A pdb=" N ILE A 413 " --> pdb=" O VAL A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 433 No H-bonds generated for 'chain 'A' and resid 431 through 433' Processing helix chain 'A' and resid 440 through 442 No H-bonds generated for 'chain 'A' and resid 440 through 442' Processing helix chain 'A' and resid 461 through 463 No H-bonds generated for 'chain 'A' and resid 461 through 463' Processing helix chain 'A' and resid 471 through 476 Processing helix chain 'A' and resid 478 through 480 No H-bonds generated for 'chain 'A' and resid 478 through 480' Processing helix chain 'A' and resid 512 through 519 Processing helix chain 'A' and resid 537 through 549 removed outlier: 3.994A pdb=" N VAL A 542 " --> pdb=" O SER A 538 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN A 543 " --> pdb=" O GLU A 539 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU A 544 " --> pdb=" O SER A 540 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA A 545 " --> pdb=" O ILE A 541 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL A 549 " --> pdb=" O ALA A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 604 Processing helix chain 'A' and resid 621 through 631 removed outlier: 3.606A pdb=" N HIS A 625 " --> pdb=" O THR A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 678 removed outlier: 3.681A pdb=" N LEU A 677 " --> pdb=" O PHE A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 700 No H-bonds generated for 'chain 'A' and resid 698 through 700' Processing helix chain 'A' and resid 702 through 716 removed outlier: 3.563A pdb=" N VAL A 707 " --> pdb=" O THR A 703 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER A 709 " --> pdb=" O ALA A 705 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET A 711 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE A 712 " --> pdb=" O MET A 708 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLU A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N TYR A 716 " --> pdb=" O ILE A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 727 No H-bonds generated for 'chain 'A' and resid 724 through 727' Processing helix chain 'A' and resid 729 through 736 removed outlier: 4.592A pdb=" N TYR A 734 " --> pdb=" O TYR A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 749 No H-bonds generated for 'chain 'A' and resid 746 through 749' Processing helix chain 'A' and resid 762 through 771 removed outlier: 3.993A pdb=" N ALA A 770 " --> pdb=" O MET A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 779 No H-bonds generated for 'chain 'A' and resid 776 through 779' Processing helix chain 'A' and resid 782 through 784 No H-bonds generated for 'chain 'A' and resid 782 through 784' Processing helix chain 'A' and resid 801 through 804 No H-bonds generated for 'chain 'A' and resid 801 through 804' Processing helix chain 'A' and resid 809 through 812 No H-bonds generated for 'chain 'A' and resid 809 through 812' Processing helix chain 'A' and resid 814 through 817 No H-bonds generated for 'chain 'A' and resid 814 through 817' Processing helix chain 'A' and resid 824 through 828 Processing helix chain 'A' and resid 835 through 855 Proline residue: A 841 - end of helix removed outlier: 3.575A pdb=" N LEU A 845 " --> pdb=" O PRO A 841 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE A 848 " --> pdb=" O VAL A 844 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN A 850 " --> pdb=" O ALA A 846 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLN A 851 " --> pdb=" O ASN A 847 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 852 " --> pdb=" O PHE A 848 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER A 853 " --> pdb=" O ALA A 849 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LEU A 854 " --> pdb=" O GLN A 850 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LYS A 855 " --> pdb=" O GLN A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 874 removed outlier: 4.164A pdb=" N HIS A 865 " --> pdb=" O THR A 861 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA A 866 " --> pdb=" O ALA A 862 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LYS A 867 " --> pdb=" O LYS A 863 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N THR A 868 " --> pdb=" O ALA A 864 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N SER A 869 " --> pdb=" O HIS A 865 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE A 871 " --> pdb=" O LYS A 867 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A 872 " --> pdb=" O THR A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 882 No H-bonds generated for 'chain 'A' and resid 879 through 882' Processing helix chain 'A' and resid 884 through 886 No H-bonds generated for 'chain 'A' and resid 884 through 886' Processing helix chain 'A' and resid 890 through 893 No H-bonds generated for 'chain 'A' and resid 890 through 893' Processing helix chain 'A' and resid 901 through 904 No H-bonds generated for 'chain 'A' and resid 901 through 904' Processing helix chain 'A' and resid 909 through 920 removed outlier: 3.772A pdb=" N GLY A 914 " --> pdb=" O SER A 910 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE A 915 " --> pdb=" O GLN A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 925 No H-bonds generated for 'chain 'A' and resid 922 through 925' Processing helix chain 'A' and resid 928 through 938 removed outlier: 3.574A pdb=" N LEU A 938 " --> pdb=" O TYR A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 950 through 963 removed outlier: 3.528A pdb=" N VAL A 955 " --> pdb=" O LYS A 951 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 956 " --> pdb=" O VAL A 952 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA A 960 " --> pdb=" O LEU A 956 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER A 962 " --> pdb=" O ILE A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 974 No H-bonds generated for 'chain 'A' and resid 971 through 974' Processing helix chain 'A' and resid 1055 through 1058 No H-bonds generated for 'chain 'A' and resid 1055 through 1058' Processing helix chain 'A' and resid 1076 through 1078 No H-bonds generated for 'chain 'A' and resid 1076 through 1078' Processing helix chain 'A' and resid 1081 through 1087 removed outlier: 3.980A pdb=" N LEU A1086 " --> pdb=" O LYS A1082 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LYS A1087 " --> pdb=" O SER A1083 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1122 removed outlier: 4.421A pdb=" N ASP A1120 " --> pdb=" O SER A1116 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A1121 " --> pdb=" O GLU A1117 " (cutoff:3.500A) Processing helix chain 'A' and resid 1128 through 1132 Processing helix chain 'A' and resid 1151 through 1165 removed outlier: 3.780A pdb=" N GLN A1155 " --> pdb=" O GLY A1151 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG A1156 " --> pdb=" O GLY A1152 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE A1157 " --> pdb=" O GLN A1153 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA A1158 " --> pdb=" O LYS A1154 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA A1160 " --> pdb=" O ARG A1156 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA A1162 " --> pdb=" O ALA A1158 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A1164 " --> pdb=" O ALA A1160 " (cutoff:3.500A) Processing helix chain 'A' and resid 1190 through 1193 No H-bonds generated for 'chain 'A' and resid 1190 through 1193' Processing helix chain 'A' and resid 1241 through 1248 removed outlier: 3.956A pdb=" N LEU A1247 " --> pdb=" O ARG A1243 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLN A1248 " --> pdb=" O LEU A1244 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 365 through 368 removed outlier: 3.847A pdb=" N GLN A 423 " --> pdb=" O LYS A 368 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 397 through 399 removed outlier: 3.672A pdb=" N ALA A 572 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL A 399 " --> pdb=" O ALA A 572 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 443 through 446 removed outlier: 7.402A pdb=" N ILE A 524 " --> pdb=" O GLY A 444 " (cutoff:3.500A) removed outlier: 8.900A pdb=" N VAL A 446 " --> pdb=" O ILE A 524 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N LEU A 526 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THR A 554 " --> pdb=" O LEU A 525 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N LEU A 527 " --> pdb=" O THR A 554 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N VAL A 556 " --> pdb=" O LEU A 527 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 1088 through 1090 removed outlier: 6.288A pdb=" N VAL A1169 " --> pdb=" O GLY A1089 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N THR A1199 " --> pdb=" O LEU A1170 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 1216 through 1220 removed outlier: 4.247A pdb=" N GLU A1226 " --> pdb=" O VAL A1218 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N GLN A1220 " --> pdb=" O ILE A1224 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ILE A1224 " --> pdb=" O GLN A1220 " (cutoff:3.500A) 140 hydrogen bonds defined for protein. 393 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: 2.27 Time building geometry restraints manager: 3.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1549 1.32 - 1.44: 2513 1.44 - 1.56: 5394 1.56 - 1.69: 1 1.69 - 1.81: 67 Bond restraints: 9524 Sorted by residual: bond pdb=" CA ILE A 195 " pdb=" C ILE A 195 " ideal model delta sigma weight residual 1.520 1.536 -0.016 8.80e-03 1.29e+04 3.27e+00 bond pdb=" C ALA A 668 " pdb=" N PRO A 669 " ideal model delta sigma weight residual 1.332 1.351 -0.019 1.30e-02 5.92e+03 2.19e+00 bond pdb=" C ILE A 195 " pdb=" N PRO A 196 " ideal model delta sigma weight residual 1.334 1.345 -0.012 8.40e-03 1.42e+04 1.98e+00 bond pdb=" CB PRO A 56 " pdb=" CG PRO A 56 " ideal model delta sigma weight residual 1.492 1.429 0.063 5.00e-02 4.00e+02 1.59e+00 bond pdb=" N VAL A 605 " pdb=" CA VAL A 605 " ideal model delta sigma weight residual 1.458 1.482 -0.024 1.90e-02 2.77e+03 1.56e+00 ... (remaining 9519 not shown) Histogram of bond angle deviations from ideal: 89.59 - 98.48: 6 98.48 - 107.38: 278 107.38 - 116.27: 5919 116.27 - 125.16: 6578 125.16 - 134.05: 117 Bond angle restraints: 12898 Sorted by residual: angle pdb=" C ASN A1126 " pdb=" CA ASN A1126 " pdb=" CB ASN A1126 " ideal model delta sigma weight residual 110.26 89.59 20.67 1.50e+00 4.44e-01 1.90e+02 angle pdb=" N ASN A1126 " pdb=" CA ASN A1126 " pdb=" C ASN A1126 " ideal model delta sigma weight residual 109.59 91.32 18.27 1.47e+00 4.63e-01 1.54e+02 angle pdb=" N ARG A 653 " pdb=" CA ARG A 653 " pdb=" CB ARG A 653 " ideal model delta sigma weight residual 110.39 90.68 19.71 1.59e+00 3.96e-01 1.54e+02 angle pdb=" C PHE A 69 " pdb=" CA PHE A 69 " pdb=" CB PHE A 69 " ideal model delta sigma weight residual 110.70 131.83 -21.13 1.83e+00 2.99e-01 1.33e+02 angle pdb=" N GLY A 652 " pdb=" CA GLY A 652 " pdb=" C GLY A 652 " ideal model delta sigma weight residual 113.18 92.01 21.17 2.37e+00 1.78e-01 7.98e+01 ... (remaining 12893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.44: 5603 26.44 - 52.89: 97 52.89 - 79.33: 13 79.33 - 105.77: 2 105.77 - 132.21: 1 Dihedral angle restraints: 5716 sinusoidal: 2228 harmonic: 3488 Sorted by residual: dihedral pdb=" C ASN A1126 " pdb=" N ASN A1126 " pdb=" CA ASN A1126 " pdb=" CB ASN A1126 " ideal model delta harmonic sigma weight residual -122.60 -90.00 -32.60 0 2.50e+00 1.60e-01 1.70e+02 dihedral pdb=" C PHE A 69 " pdb=" N PHE A 69 " pdb=" CA PHE A 69 " pdb=" CB PHE A 69 " ideal model delta harmonic sigma weight residual -122.60 -151.08 28.48 0 2.50e+00 1.60e-01 1.30e+02 dihedral pdb=" N ALA A1127 " pdb=" C ALA A1127 " pdb=" CA ALA A1127 " pdb=" CB ALA A1127 " ideal model delta harmonic sigma weight residual 122.90 99.33 23.57 0 2.50e+00 1.60e-01 8.89e+01 ... (remaining 5713 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.208: 1481 0.208 - 0.417: 7 0.417 - 0.625: 1 0.625 - 0.834: 2 0.834 - 1.042: 1 Chirality restraints: 1492 Sorted by residual: chirality pdb=" CA PHE A 69 " pdb=" N PHE A 69 " pdb=" C PHE A 69 " pdb=" CB PHE A 69 " both_signs ideal model delta sigma weight residual False 2.51 1.47 1.04 2.00e-01 2.50e+01 2.71e+01 chirality pdb=" CA ASN A1126 " pdb=" N ASN A1126 " pdb=" C ASN A1126 " pdb=" CB ASN A1126 " both_signs ideal model delta sigma weight residual False 2.51 3.26 -0.75 2.00e-01 2.50e+01 1.42e+01 chirality pdb=" CA ALA A1127 " pdb=" N ALA A1127 " pdb=" C ALA A1127 " pdb=" CB ALA A1127 " both_signs ideal model delta sigma weight residual False 2.48 3.14 -0.66 2.00e-01 2.50e+01 1.08e+01 ... (remaining 1489 not shown) Planarity restraints: 1640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 681 " -0.072 5.00e-02 4.00e+02 1.09e-01 1.92e+01 pdb=" N PRO A 682 " 0.189 5.00e-02 4.00e+02 pdb=" CA PRO A 682 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO A 682 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 701 " -0.045 5.00e-02 4.00e+02 6.73e-02 7.24e+00 pdb=" N PRO A 702 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 702 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 702 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 195 " 0.042 5.00e-02 4.00e+02 6.28e-02 6.30e+00 pdb=" N PRO A 196 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 196 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 196 " 0.035 5.00e-02 4.00e+02 ... (remaining 1637 not shown) Histogram of nonbonded interaction distances: 1.00 - 1.78: 2 1.78 - 2.56: 55 2.56 - 3.34: 10804 3.34 - 4.12: 20476 4.12 - 4.90: 38187 Nonbonded interactions: 69524 Sorted by model distance: nonbonded pdb=" O ASN A1126 " pdb=" OD1 ASN A1126 " model vdw 1.004 3.040 nonbonded pdb=" O ASN A1126 " pdb=" CG ASN A1126 " model vdw 1.707 3.270 nonbonded pdb=" C ASN A1126 " pdb=" OD1 ASN A1126 " model vdw 2.081 3.270 nonbonded pdb=" OG SER A 697 " pdb=" O ALA A 744 " model vdw 2.274 2.440 nonbonded pdb=" OE2 GLU A 829 " pdb=" OG SER A 944 " model vdw 2.335 2.440 ... (remaining 69519 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=1.00 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: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.070 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 27.440 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 9524 Z= 0.302 Angle : 1.036 21.171 12898 Z= 0.592 Chirality : 0.067 1.042 1492 Planarity : 0.007 0.109 1640 Dihedral : 11.185 132.215 3488 Min Nonbonded Distance : 1.004 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Cbeta Deviations : 0.45 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: -6.42 (0.15), residues: 1213 helix: -4.87 (0.07), residues: 634 sheet: -3.52 (0.50), residues: 72 loop : -3.31 (0.22), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 933 HIS 0.010 0.002 HIS A 51 PHE 0.026 0.002 PHE A 69 TYR 0.016 0.002 TYR A 730 ARG 0.006 0.001 ARG A 295 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 1.026 Fit side-chains revert: symmetry clash REVERT: A 37 ASP cc_start: 0.8607 (m-30) cc_final: 0.8382 (m-30) REVERT: A 218 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7624 (tm-30) REVERT: A 543 GLN cc_start: 0.9035 (tp-100) cc_final: 0.8467 (tp-100) REVERT: A 708 MET cc_start: 0.8645 (tmm) cc_final: 0.8406 (tmm) REVERT: A 1006 ILE cc_start: 0.8354 (mm) cc_final: 0.8063 (tp) REVERT: A 1026 MET cc_start: 0.6611 (mmm) cc_final: 0.6287 (mmm) REVERT: A 1156 ARG cc_start: 0.8362 (mtt-85) cc_final: 0.7493 (tpp80) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.2910 time to fit residues: 70.9276 Evaluate side-chains 107 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 0.4980 chunk 91 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 61 optimal weight: 7.9990 chunk 48 optimal weight: 8.9990 chunk 94 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 20.0000 chunk 70 optimal weight: 2.9990 chunk 109 optimal weight: 7.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 HIS A 168 HIS ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 503 GLN A 602 GLN A 758 ASN A1041 GLN A1205 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 9524 Z= 0.239 Angle : 0.623 9.558 12898 Z= 0.338 Chirality : 0.043 0.166 1492 Planarity : 0.005 0.086 1640 Dihedral : 6.939 62.183 1407 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 2.04 % Allowed : 7.14 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.58 (0.18), residues: 1213 helix: -4.17 (0.11), residues: 638 sheet: -3.17 (0.53), residues: 72 loop : -2.89 (0.25), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 283 HIS 0.005 0.001 HIS A 784 PHE 0.025 0.002 PHE A1130 TYR 0.014 0.001 TYR A 740 ARG 0.005 0.000 ARG A 725 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 114 time to evaluate : 0.996 Fit side-chains revert: symmetry clash REVERT: A 218 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7627 (tm-30) REVERT: A 1006 ILE cc_start: 0.8287 (mm) cc_final: 0.7962 (tp) REVERT: A 1070 MET cc_start: 0.8333 (tpt) cc_final: 0.8058 (tpp) outliers start: 20 outliers final: 6 residues processed: 131 average time/residue: 0.2285 time to fit residues: 41.4671 Evaluate side-chains 98 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 92 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 973 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 98 optimal weight: 7.9990 chunk 109 optimal weight: 6.9990 chunk 37 optimal weight: 0.0040 chunk 88 optimal weight: 1.9990 overall best weight: 1.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 748 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 9524 Z= 0.319 Angle : 0.648 13.925 12898 Z= 0.342 Chirality : 0.044 0.149 1492 Planarity : 0.005 0.080 1640 Dihedral : 6.641 52.146 1407 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 2.14 % Allowed : 9.48 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: -5.01 (0.19), residues: 1213 helix: -3.59 (0.14), residues: 644 sheet: -3.23 (0.51), residues: 82 loop : -2.69 (0.26), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 283 HIS 0.003 0.001 HIS A 937 PHE 0.029 0.002 PHE A 438 TYR 0.014 0.002 TYR A 740 ARG 0.004 0.000 ARG A1123 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 105 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.7847 (mttp) cc_final: 0.7580 (pttm) REVERT: A 218 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7624 (tm-30) REVERT: A 429 VAL cc_start: 0.9342 (t) cc_final: 0.9116 (m) REVERT: A 1014 HIS cc_start: 0.8169 (m90) cc_final: 0.7646 (m-70) outliers start: 21 outliers final: 12 residues processed: 120 average time/residue: 0.2450 time to fit residues: 40.4278 Evaluate side-chains 99 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 87 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1063 ASP Chi-restraints excluded: chain A residue 1074 LYS Chi-restraints excluded: chain A residue 1120 ASP Chi-restraints excluded: chain A residue 1203 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.7980 chunk 82 optimal weight: 0.5980 chunk 57 optimal weight: 30.0000 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 0.0050 chunk 73 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 GLN A 784 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9524 Z= 0.186 Angle : 0.565 11.804 12898 Z= 0.299 Chirality : 0.041 0.142 1492 Planarity : 0.004 0.075 1640 Dihedral : 6.090 47.636 1407 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 2.24 % Allowed : 11.21 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.43 (0.21), residues: 1213 helix: -3.14 (0.16), residues: 640 sheet: -2.92 (0.56), residues: 71 loop : -2.42 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 185 HIS 0.002 0.000 HIS A 937 PHE 0.024 0.001 PHE A1130 TYR 0.012 0.001 TYR A 740 ARG 0.005 0.000 ARG A 511 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 105 time to evaluate : 1.560 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.7799 (mttp) cc_final: 0.7555 (pttm) REVERT: A 218 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7614 (tm-30) REVERT: A 238 TYR cc_start: 0.8820 (m-80) cc_final: 0.8409 (m-80) REVERT: A 543 GLN cc_start: 0.9076 (OUTLIER) cc_final: 0.8850 (tt0) REVERT: A 604 MET cc_start: 0.3770 (ttt) cc_final: 0.3164 (ptm) REVERT: A 1014 HIS cc_start: 0.8122 (m90) cc_final: 0.7509 (m-70) outliers start: 22 outliers final: 19 residues processed: 119 average time/residue: 0.2367 time to fit residues: 39.0773 Evaluate side-chains 114 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 94 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 543 GLN Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1063 ASP Chi-restraints excluded: chain A residue 1074 LYS Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1120 ASP Chi-restraints excluded: chain A residue 1149 LEU Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1215 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 87 optimal weight: 0.3980 chunk 48 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 chunk 80 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9524 Z= 0.260 Angle : 0.582 10.680 12898 Z= 0.307 Chirality : 0.042 0.139 1492 Planarity : 0.004 0.071 1640 Dihedral : 6.108 49.378 1407 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 3.16 % Allowed : 11.21 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.19 (0.21), residues: 1213 helix: -2.88 (0.17), residues: 631 sheet: -3.25 (0.49), residues: 84 loop : -2.32 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 185 HIS 0.002 0.000 HIS A 937 PHE 0.025 0.002 PHE A1130 TYR 0.013 0.001 TYR A 740 ARG 0.003 0.000 ARG A1007 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 94 time to evaluate : 1.034 Fit side-chains REVERT: A 35 LYS cc_start: 0.7795 (mttp) cc_final: 0.7562 (pttm) REVERT: A 218 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7619 (tm-30) REVERT: A 238 TYR cc_start: 0.8852 (m-80) cc_final: 0.8474 (m-80) REVERT: A 543 GLN cc_start: 0.9077 (tp40) cc_final: 0.8729 (tp-100) REVERT: A 604 MET cc_start: 0.3755 (ttt) cc_final: 0.3189 (ptm) REVERT: A 1014 HIS cc_start: 0.8109 (m90) cc_final: 0.7489 (m-70) REVERT: A 1070 MET cc_start: 0.8629 (tpt) cc_final: 0.8389 (tpp) outliers start: 31 outliers final: 24 residues processed: 116 average time/residue: 0.2287 time to fit residues: 37.0694 Evaluate side-chains 107 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 83 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 734 TYR Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1063 ASP Chi-restraints excluded: chain A residue 1074 LYS Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1120 ASP Chi-restraints excluded: chain A residue 1149 LEU Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain A residue 1215 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 117 optimal weight: 0.0060 chunk 97 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 0.5980 chunk 112 optimal weight: 3.9990 overall best weight: 1.4400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9524 Z= 0.259 Angle : 0.587 9.764 12898 Z= 0.307 Chirality : 0.042 0.153 1492 Planarity : 0.004 0.073 1640 Dihedral : 6.065 49.056 1407 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 2.85 % Allowed : 12.03 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.03 (0.22), residues: 1213 helix: -2.74 (0.17), residues: 636 sheet: -3.09 (0.50), residues: 83 loop : -2.26 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 185 HIS 0.002 0.000 HIS A 937 PHE 0.026 0.001 PHE A1130 TYR 0.013 0.001 TYR A 740 ARG 0.005 0.000 ARG A 384 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 80 time to evaluate : 1.129 Fit side-chains REVERT: A 35 LYS cc_start: 0.7801 (mttp) cc_final: 0.7577 (pttm) REVERT: A 218 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7657 (tm-30) REVERT: A 238 TYR cc_start: 0.8896 (m-80) cc_final: 0.8514 (m-80) REVERT: A 543 GLN cc_start: 0.9112 (tp40) cc_final: 0.8753 (tp40) REVERT: A 604 MET cc_start: 0.3726 (ttt) cc_final: 0.3196 (ptm) REVERT: A 1014 HIS cc_start: 0.8097 (m90) cc_final: 0.7526 (m-70) outliers start: 28 outliers final: 23 residues processed: 100 average time/residue: 0.2352 time to fit residues: 33.8737 Evaluate side-chains 99 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 76 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 734 TYR Chi-restraints excluded: chain A residue 959 THR Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1074 LYS Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1120 ASP Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain A residue 1215 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 0.0470 chunk 66 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 98 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.9882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 503 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9524 Z= 0.192 Angle : 0.541 8.730 12898 Z= 0.285 Chirality : 0.041 0.140 1492 Planarity : 0.004 0.070 1640 Dihedral : 5.837 47.320 1407 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 2.75 % Allowed : 12.44 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.75 (0.22), residues: 1213 helix: -2.50 (0.18), residues: 627 sheet: -2.81 (0.52), residues: 84 loop : -2.19 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 185 HIS 0.002 0.000 HIS A 937 PHE 0.026 0.001 PHE A1130 TYR 0.013 0.001 TYR A 740 ARG 0.005 0.000 ARG A 384 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 83 time to evaluate : 1.135 Fit side-chains REVERT: A 35 LYS cc_start: 0.7801 (mttp) cc_final: 0.7588 (pttm) REVERT: A 218 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7669 (tm-30) REVERT: A 238 TYR cc_start: 0.8920 (m-80) cc_final: 0.8578 (m-80) REVERT: A 384 ARG cc_start: 0.8111 (ttm-80) cc_final: 0.7909 (tpp80) REVERT: A 543 GLN cc_start: 0.9124 (tp40) cc_final: 0.8750 (tp40) REVERT: A 604 MET cc_start: 0.3684 (ttt) cc_final: 0.3206 (ptm) REVERT: A 1014 HIS cc_start: 0.8010 (m90) cc_final: 0.7479 (m-70) outliers start: 27 outliers final: 25 residues processed: 102 average time/residue: 0.2238 time to fit residues: 32.5656 Evaluate side-chains 102 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 77 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 734 TYR Chi-restraints excluded: chain A residue 959 THR Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 991 THR Chi-restraints excluded: chain A residue 1063 ASP Chi-restraints excluded: chain A residue 1074 LYS Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1120 ASP Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain A residue 1215 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 chunk 111 optimal weight: 9.9990 chunk 101 optimal weight: 20.0000 chunk 108 optimal weight: 0.5980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 9524 Z= 0.353 Angle : 0.618 8.427 12898 Z= 0.325 Chirality : 0.044 0.138 1492 Planarity : 0.004 0.073 1640 Dihedral : 6.238 51.104 1407 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.40 % Favored : 90.60 % Rotamer: Outliers : 3.16 % Allowed : 12.74 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.82 (0.22), residues: 1213 helix: -2.58 (0.18), residues: 636 sheet: -2.62 (0.54), residues: 85 loop : -2.22 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 185 HIS 0.003 0.001 HIS A 168 PHE 0.028 0.002 PHE A1130 TYR 0.013 0.002 TYR A 740 ARG 0.004 0.000 ARG A1007 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 81 time to evaluate : 1.076 Fit side-chains REVERT: A 35 LYS cc_start: 0.7783 (mttp) cc_final: 0.7575 (pttm) REVERT: A 218 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7699 (tm-30) REVERT: A 238 TYR cc_start: 0.8873 (m-80) cc_final: 0.8421 (m-80) REVERT: A 543 GLN cc_start: 0.9111 (OUTLIER) cc_final: 0.8752 (tp40) REVERT: A 604 MET cc_start: 0.3733 (ttt) cc_final: 0.3225 (ptm) REVERT: A 1014 HIS cc_start: 0.7975 (m90) cc_final: 0.7425 (m-70) outliers start: 31 outliers final: 22 residues processed: 101 average time/residue: 0.2318 time to fit residues: 33.5798 Evaluate side-chains 102 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 79 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 543 GLN Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 734 TYR Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 959 THR Chi-restraints excluded: chain A residue 991 THR Chi-restraints excluded: chain A residue 1074 LYS Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain A residue 1215 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 10.0000 chunk 65 optimal weight: 0.9980 chunk 47 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9524 Z= 0.250 Angle : 0.577 7.977 12898 Z= 0.304 Chirality : 0.042 0.143 1492 Planarity : 0.004 0.077 1640 Dihedral : 6.073 48.970 1407 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 2.55 % Allowed : 13.86 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.66 (0.22), residues: 1213 helix: -2.45 (0.18), residues: 629 sheet: -2.56 (0.54), residues: 85 loop : -2.14 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 185 HIS 0.002 0.000 HIS A 168 PHE 0.027 0.001 PHE A1130 TYR 0.013 0.001 TYR A 740 ARG 0.004 0.000 ARG A1007 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 82 time to evaluate : 1.089 Fit side-chains REVERT: A 218 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7692 (tm-30) REVERT: A 238 TYR cc_start: 0.8924 (m-80) cc_final: 0.8619 (m-80) REVERT: A 543 GLN cc_start: 0.9124 (tp40) cc_final: 0.8713 (tp40) REVERT: A 576 GLN cc_start: 0.8210 (pm20) cc_final: 0.7596 (tm-30) REVERT: A 604 MET cc_start: 0.3684 (ttt) cc_final: 0.3222 (ptm) REVERT: A 1014 HIS cc_start: 0.8004 (m90) cc_final: 0.7460 (m-70) REVERT: A 1070 MET cc_start: 0.8547 (tpt) cc_final: 0.8192 (tpp) REVERT: A 1093 GLN cc_start: 0.6088 (tp40) cc_final: 0.5821 (tp40) REVERT: A 1195 MET cc_start: 0.7148 (mtt) cc_final: 0.6779 (mtt) outliers start: 25 outliers final: 24 residues processed: 100 average time/residue: 0.2310 time to fit residues: 32.3683 Evaluate side-chains 101 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 77 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 734 TYR Chi-restraints excluded: chain A residue 959 THR Chi-restraints excluded: chain A residue 991 THR Chi-restraints excluded: chain A residue 1074 LYS Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain A residue 1215 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 0.0010 chunk 79 optimal weight: 0.6980 chunk 120 optimal weight: 10.0000 chunk 110 optimal weight: 6.9990 chunk 95 optimal weight: 0.0050 chunk 9 optimal weight: 1.9990 chunk 74 optimal weight: 0.0980 chunk 58 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 GLN ** A1250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9524 Z= 0.140 Angle : 0.516 8.576 12898 Z= 0.273 Chirality : 0.040 0.149 1492 Planarity : 0.003 0.073 1640 Dihedral : 5.604 45.604 1407 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 2.45 % Allowed : 14.37 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.23), residues: 1213 helix: -2.08 (0.20), residues: 612 sheet: -2.00 (0.60), residues: 75 loop : -2.07 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 185 HIS 0.001 0.000 HIS A1128 PHE 0.025 0.001 PHE A1130 TYR 0.012 0.001 TYR A 740 ARG 0.004 0.000 ARG A1007 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 85 time to evaluate : 1.094 Fit side-chains revert: symmetry clash REVERT: A 218 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7623 (tm-30) REVERT: A 543 GLN cc_start: 0.9114 (OUTLIER) cc_final: 0.8762 (tp40) REVERT: A 576 GLN cc_start: 0.8163 (pm20) cc_final: 0.7594 (tm-30) REVERT: A 1014 HIS cc_start: 0.8045 (m90) cc_final: 0.7503 (m-70) REVERT: A 1070 MET cc_start: 0.8543 (tpt) cc_final: 0.8237 (tpp) REVERT: A 1123 ARG cc_start: 0.7214 (mtt180) cc_final: 0.6921 (mtt180) outliers start: 24 outliers final: 20 residues processed: 101 average time/residue: 0.2526 time to fit residues: 35.6558 Evaluate side-chains 101 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 80 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 543 GLN Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 734 TYR Chi-restraints excluded: chain A residue 870 MET Chi-restraints excluded: chain A residue 959 THR Chi-restraints excluded: chain A residue 991 THR Chi-restraints excluded: chain A residue 1074 LYS Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain A residue 1215 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 40 optimal weight: 0.0470 chunk 98 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 17 optimal weight: 0.0010 chunk 84 optimal weight: 0.3980 chunk 5 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.4484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 GLN ** A1250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.193155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.143888 restraints weight = 12309.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.143161 restraints weight = 8041.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.144084 restraints weight = 5821.687| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9524 Z= 0.128 Angle : 0.517 8.795 12898 Z= 0.274 Chirality : 0.040 0.147 1492 Planarity : 0.003 0.068 1640 Dihedral : 5.492 45.230 1407 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 2.04 % Allowed : 15.29 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.23), residues: 1213 helix: -1.83 (0.20), residues: 610 sheet: -1.95 (0.61), residues: 77 loop : -2.10 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 283 HIS 0.001 0.000 HIS A 937 PHE 0.032 0.001 PHE A1130 TYR 0.013 0.001 TYR A 740 ARG 0.005 0.000 ARG A1078 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1964.28 seconds wall clock time: 36 minutes 28.01 seconds (2188.01 seconds total)